InfraLife Feasibility Call Sparks New Collaborations in Life Science

InfraLife has successfully concluded its final initiative—a feasibility call designed to boost the use of Sweden’s leading research infrastructures and foster collaboration in life sciences. Despite modest funding, the call delivered exciting results and laid the groundwork for future partnerships between researchers and Sweden’s world-class infrastructures. New workflows of method integration and method combination were established, new structures were identified and the foundation for potential drug targets were investigated. This highlights the potential of cross-infrastructure partnerships to push the boundaries of life science research.

An open call to Swedish researchers to facilitate the use of InfraLife’s large scale research infrastructures

The call, open to researchers across Sweden, required applicants to involve at least two InfraLife infrastructures in their projects. Seven applications were reviewed by representatives from MAX IV, SciLifeLab and ESS. Of these seven, four projects, which were proof of concept or exploratory in nature, were selected and awarded 600,000 SEK in total. This initiative marked the conclusion of the four-year InfraLife project (2021–2025), which aimed to showcase infrastructure capabilities, attract new users, and promote technology development and collaboration.

Method integration to gain elemental and spatial information

Project 1: Spatial biology across scales and matters-combining omics with element distribution and structure.

Researchers from SciLifeLab and MAX IV were first connected during an InfraLife Exchange Dialogue on Spatial Biology to learn about each other’s techniques. It became apparent that there was a mutual interest in analysing samples using both techniques in a bid to get complimentary information. The InfraLife feasibility call allowed the researchers to test various innovative approaches in sample preparation and analysis using Nano-XRF and infrared spectroscopy (O-PTIR) at MAX IV with Spatial Proteomics at SciLifeLab. Results showed that no single method could address all research needs, and despite two experiments taking place at MAX IV, each one had different requirements before being tested at SciLifeLab. The results allowed the researchers to look at element distribution, structure and spatial proteomics data in the same sample. This kind of holistic, multi-modal approach exemplifies the core vision of InfraLife: leveraging synergy between different infrastructures to study complex life-science questions.

Figure 1. Phenocycler data (left) from a lung section and Nano-XRF data (right) from a consecutive section.

Structure-aided drug design for respiratory disease

Project 2: Structural basis for the role of angiotensin-converting enzyme 2 (ACE2) as a novel regulator of transmembrane serine protease 2 (TMPRSS2) catalyzed proteolytic activation of outer structural proteins of respiratory viruses.

The aim of the project was to determine the structural basis by which ACE2 increases the activity of the protease TMPRSS2, which is involved in several respiratory diseases. TMPRSS2 causes proteolytic cleavage of viral envelope proteins which is essential for the infectivity of many viruses, hence providing a potential drug target. To advance this research, the Lund Protein Production (LP3) facility was used to produce the ectodomains of TMPRSS2 and ACE2 enabling affinity testing between the two proteins. Following this, hydrogen-deuterium (H/D) exchange mass spectrometry at the Structural Proteomics unit of SciLifeLab identifed regions of particular interest in both ACE2 and TMPRSS2 providing the information needed to produce varients of both. Currently these varients, along with additional samples, are awaiting further structural analysis through X-ray crystallography at BioMAX at MAX IV and Cryo-EM methods from SciLifeLab. Understanding more about the mechanism between ACE2 and TMPRSS2 opens up a new modality to combat viral infections by aiding structure-based drug design.

Figure 2. The arrow indicates two connected and surface exposed parts of ACE2 potentially interacting with TMPRSS2 as identified by HD-MS. ACE2 structure from PDB 1R42.

Integrated workflows for antiviral drug discovery

Project 3: Crystallographic fragment screening combined with in silico design to identify novel antivirals.

The project established integrated workflows for structure-based drug design against flaviviruses by identifying novel inhibitor candidates and developing fragment-to-lead protocols across infrastructures. A crystallographic screen of 577 compounds was conducted at the fragment crystallographic screening platform FragMAX at MAX IV using fragment sets from the Chemical Biology Consortium Sweden (CBCS) unit of SciLifeLab and Uppsala University. Eleven fragments were discovered, undergoing DSF assay at CBCS which resulted in more than 20 identified hits shipped to MAX IV for X-ray crystallography. In parallel, these 11 fragment hits underwent a virtual screening resulting in more than 60 selected compounds for follow up experiments. Throughout this collaboration protocols and workflows were developed to combine crystallographic fragment screening with computational chemistry, compound management and assays, providing starting points for antiviral lead progression suitable for follow-up campaigns. The choice of such a project aligns well with InfraLife’s goal of enabling complex workflows that combine complementary technologies.

Figure 3. Project work plan across MAX IV, CBCS and UU.

Using integrated structural biology to explore the apoptotic cascade

Project 4: How the HtrA2:XIAP interplay initiates the apoptotic cascade.

This study focuses on the human mitochondrial serine protease HtrA2 and its role in cleaving inhibitor of apoptosis proteins (IAP), a central process to the apoptotic cascade. This project sought to obtain a structural model of the HtrA2.XIAP complex using an integrated structural biology approach by researchers in GU. Small angle scattering (SAXS) experiments at MAX IV provided important overall structural information of the complete HtrA2:XIAP complex. The next method employed was Structural Proteomics at SciLifeLab, where the stability of the amino terminal helix was observed. This feature is proposed to be highly flexible upon activation, thus suggesting that structural proteomics has the potential to delineate important steps within the activation cycle of this important protease. Samples have been prepared and are awaiting analysis by solid-state NMR spectroscopy in the SciLifeLab Umeå node, which will provide even further integrated structural biology information.

Figure 4. Overall coverage of Structural Proteomics hydrogen-deuterium exchange plotted on the
sequence.

Collaboration to form, develop and deepen connections

The InfraLife feasibility call fostered collaboration between the infrastructures that might not have occurred otherwise. Each project have various levels and forms of collaboration. Project 1 held multiple meetings, Exchange Dialogues and presented together at the MAX IV User Meeting. Project 2 expanded from five to seven researchers and included infrastructures outside of InfraLife’s three and groups outside of Sweden. Project 3 established a new strong collaboration and used the funding to align their complementary services. Project 4 strengthen collaborations between infrastructures and research groups and deepened existing connections.

Beyond the call: grants, manuscripts and joint services

The small-scale, feasibility nature of the funding made it possible for early-stage, high-risk or unconventional projects to be tested quickly and efficiently. This lowers the entry barrier for researchers to try out integrative ideas — which if successful, can lead to larger grants, more robust collaborations, and ultimately, new scientific discoveries or applications. Each of the projects has inititated plans beyond this call. Project 1 will submit a methods manuscript and apply for larger funding grants. Project 2 has samples awaiting further structural analysis which could aid drug development strategies. Project 3 has been awarded additional funding and will maintain and expand their joint service portfolio providing seamless crystallographic, biochemical, and computational capabilities for future academic projects. Project 4 has submitted two joint funding applications to further facilitate integrated structural biology research. The InfraLife feasibility call was more than a small-funding mechanism: it was a strategic tool to build momentum and capacity for cross-infrastructure, cross-disciplinary research.