Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system

Alexander Van de Steen; Rana Khalife; Noelle Colant; Hasan Mustafa Khan; Matas Deveikis; Saverio Charalambous; Clare M Robinson; Rupali Dabas; Sofia Esteban Serna; Diana A Catana; Konstantin Pildish; Vladimir Kalinovskiy; Kenth Gustafsson; Stefanie Frank

doi:10.1016/j.synbio.2021.09.001

Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system

Synth Syst Biotechnol. 2021 Sep 9;6(3):231-241. doi: 10.1016/j.synbio.2021.09.001. eCollection 2021 Sep.

Authors

Alexander Van de Steen¹, Rana Khalife¹, Noelle Colant¹, Hasan Mustafa Khan¹, Matas Deveikis^{1

2}, Saverio Charalambous^{1

2}, Clare M Robinson^{3

2}, Rupali Dabas^{3

2}, Sofia Esteban Serna^{4

2}, Diana A Catana^{4

2}, Konstantin Pildish^{4

2}, Vladimir Kalinovskiy^{4

2}, Kenth Gustafsson¹, Stefanie Frank¹

Affiliations

¹ Department of Biochemical Engineering, University College London, UK.
² UCL iGEM Student Team 2019, UK.
³ Natural Sciences, University College London, UK.
⁴ Division of Biosciences, University College London, UK.

Abstract

The development of Drug Delivery Systems (DDS) has led to increasingly efficient therapies for the treatment and detection of various diseases. DDS use a range of nanoscale delivery platforms produced from polymeric of inorganic materials, such as micelles, and metal and polymeric nanoparticles, but their variant chemical composition make alterations to their size, shape, or structures inherently complex. Genetically encoded protein nanocages are highly promising DDS candidates because of their modular composition, ease of recombinant production in a range of hosts, control over assembly and loading of cargo molecules and biodegradability. One example of naturally occurring nanocompartments are encapsulins, recently discovered bacterial organelles that have been shown to be reprogrammable as nanobioreactors and vaccine candidates. Here we report the design and application of a targeted DDS platform based on the Thermotoga maritima encapsulin reprogrammed to display an antibody mimic protein called Designed Ankyrin repeat protein (DARPin) on the outer surface and to encapsulate a cytotoxic payload. The DARPin9.29 chosen in this study specifically binds to human epidermal growth factor receptor 2 (HER2) on breast cancer cells, as demonstrated in an in vitro cell culture model. The encapsulin-based DDS is assembled in one step in vivo by co-expressing the encapsulin-DARPin9.29 fusion protein with an engineered flavin-binding protein mini-singlet oxygen generator (MiniSOG), from a single plasmid in Escherichia coli. Purified encapsulin-DARPin_miniSOG nanocompartments bind specifically to HER2 positive breast cancer cells and trigger apoptosis, indicating that the system is functional and specific. The DDS is modular and has the potential to form the basis of a multi-receptor targeted system by utilising the DARPin screening libraries, allowing use of new DARPins of known specificities, and through the proven flexibility of the encapsulin cargo loading mechanism, allowing selection of cargo proteins of choice.

Keywords: Annexin V-FITC, Annexin V-Fluorescein IsoThiocyanate Conjugate; Cytotoxic protein; DARPin; DARPin9.29, Designed Ankyrin Repeat Protein 9.29; DDS, Drug Delivery System; Drug delivery system; EPR, Enhanced Permeability and Retention effect; Encapsulin; HER2, Human Epidermal growth factor Receptor 2; His6, Hexahistidine; MSCs, Mesenchymal Stem Cells; NPs, NanoParticles; SK-BR-3, Sloan-Kettering Breast cancer cell line/HER2-overexpressing human breast cancer cell line; STII, StrepII-tag, an eight-residue peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) with intrinsic affinity toward streptavidin that can be fused to recombinant protein in various fashions; T. maritima, Thermotoga maritima; VLPs, Virus-Like Particle; iGEM, international Genetically Engineered Machine; iLOV, improved Light, Oxygen or Voltage-sensing flavoprotein; mScarlet, a bright monomeric red fluorescent protein; miniSOG, mini-Singlet Oxygen Generator; rTurboGFP, recombinant Turbo Green Fluorescent Protein.