One trillion photoswitchable molecular devices: a molecular foundry to control protein interactions using light

The universal ability to control (bio)molecular interactions in living or synthetic systems is a grand challenge for chemical
biology, a solution for which would have wide-ranging implications for basic biology, synthetic biology and therapeutic
discovery. Photochemical control of biomolecular interactions is an approach to this challenge which has attracted intense
recent interest. Prominent examples range from photoresponsive materials to light-responsive protein domains, and
photoswitchable ligands which can control e.g. tubulin polymerization and thus cell division in response to light, also termed
photopharmacology (exemplified by recent papers from the Trauner and Feringa labs). Whilst these examples provide proof
of principle for the importance and potential of minimally invasive control of biology using light signals, they each suffer from
significant disadvantages, for example a requirement for genetic manipulation, or a highly bespoke design which works only
for a single highly engineered system.
Here we propose to overcome the limitations of existing paradigms by developing the first discovery platform for
photoswitchable ligands to any protein of interest, enabling a plethora of new approaches including on/off switches for
enzyme activity, protein-protein interactions, and protein localisation. Combining cutting-edge hyperstable photoswitch
technology (Fuchter) with trillion-member genetically encoded cyclic peptide library synthesis (Walport) we will generate a
toolkit for the identification of ligands which can bind to a given protein in one of two switchable configurations and
demonstrate its application to a series of light-switchable protein interactions (Tate). Furthermore, the modularity of these
molecular devices will enable their use as a component in future bottom-up and top-down synthetic biology approaches,
providing post-translational control over protein function in cells or protocells. The project will address the following Aims:
1) Design, synthesise and incorporate '1st generation' synthetic diazo photoswitches into a trillion-member cyclic peptide
library using flexible in vitro translation, and select binders to a model cell surface protein (cd59) .
2) Identify selective switchable ligands which can modulate binding to cd59 and induce switchable ligand uptake in a cellular
system in response to light-induced activation.
3) Expand the universal switchable ligand platform to exemplify applications in GPCR dimerisation (FFA2), reversible cell
capture, and multicyclic peptide libraries with switchable bridges.
Achievability & Remit: This project builds on
unique capabilities of the collaborating labs,
including flexible in vitro translation
technology for RNA display of trillion-member
cyclic peptide libraries (Walport), the
discovery of hyperstable photoswitches
(Fuchter) and innovations from current ICB
CDT students in the Tate group, including the
discovery of high-affinity (non-switchable)
cd59 ligands using large scale cyclic peptide
library screens (Bickel; with Bubeck lab), and
incorporation of cell-active photoswitches in
small molecule probes (Kounde; with GSK).
We thus have in place the sophisticated
technologies on which the physical science
innovations of this project will build, including
validated cyclic peptide libraries, robust
photoswitches, and access to a series of
model systems on which to test the PhysSci
innovations. The project directly addresses
the core ICB CDT remit, including molecular
interactions (protein/ligand, protein/protein)
and incorporation of novel devices into
multiscale biological frameworks, with
significant future applications in both
bioscience and synthetic biology.

Addressing UK skills demand: The most important impact of the CDT will be to train a new generation of Chemical Biology PhD graduates (~80) to be future leaders of enterprise, molecular technology innovation and translation for academia and industry. They will be able to embrace the life science's industrialisation thereby filling a vital skills gap in UK industry. These students will be able to bridge the divide between academia/industry and development/application across the physical/mathematical sciences and life sciences, as well as the human-machine interfaces. The technology programme of the CDT will empower our students as serial inventors, not reliant on commercial solutions.
CDT Network-Communication & Engagement: The CDT will shape the landscape by bringing together >160 research groups with leading players from industry, government, tech accelerators, SMEs and CDT affiliates. The CDT is pioneering new collaboration models, from co-located prototyping warehouses through to hackathons-these will redefine industry-academic collaborations and drive technology transfer.
UK plc: The technologies generated by the CDT will produce IP with potential for direct commercial exploitation and will also provide valuable information for healthcare and industry. They will redefine the state of the art with respect to the ability to make, measure, model and manipulate molecular interactions in biological systems across multiple length scales. Coupled with industry 4.0 approaches this will reduce the massive, spiralling cost of product development pipelines. These advances will help establish the molecular engineering rules underlying challenging scientific problems in the life sciences that are currently intractable. The technology advances and the corresponding insight in biology generated will be exploitable in industrial and medical applications, resulting in enhanced capabilities for end-users in biological research, biomarker discovery, diagnostics and drug discovery.
These advances will make a significant contribution to innovation in UK industry, with a 5-10 year timeframe for commercial realisation. e.g. These tools will facilitate the identification of illness in its early stages, minimising permanent damage (10 yrs) and reducing associated healthcare costs. In the context of drug discovery, the ability to fuse the power of AI with molecular technologies that provide insight into the molecular mechanisms of disease, target and biomarker validation and testing for side effects of candidates will radically transform productivity (5-10 yrs). Developments in automation and rapid prototyping will reduce the barrier to entry for new start-ups and turn biology into an information technology driven by data, computation and high-throughput robotics. Technologies such as integrated single cell analysis and label free molecular tracking will be exploitable for clinical diagnostics and drug discovery on shorter time scales (ca.3-5 yrs).
Entrepreneurship & Exploitation: Embedded within the CDT, the DISRUPT tech-accelerator programme will drive and support the creation of a new wave of student-led spin-out vehicles based on student-owned IP.
Wider Community: The outreach, responsible research and communication skill-set of our graduates will strengthen end-user engagement outside their PhD research fields and with the general public. Many technologies developed in the CDT will address societal challenges, and thus will generate significant public interest. Through new initiatives such as the Makerspace the CDT will spearhead new citizen science approaches where the public engage directly in CDT led research by taking part in e.g hackathons. Students will also engage with a wide spectrum of stakeholders, including policy makers, regulatory bodies and end-users. e.g. the Molecular Quarter will ensure the CDT can promote new regulatory frameworks that will promote quick customer and patient access to CDT led breakthroughs.