Latest revision as of 12:34, 2 October 2024

Cathepsin B-Cleavable Linker: GFLG

This basic part encodes the GFLG peptide linker, a cathepsin B-responsive cleavage site, which can be used for targeted drug delivery or diagnostics in cancerous tissues. As a part of our PICasSO toolbox, the GFLG linker can be used for the precise control of protein activity through cleavage-induced oligomerization of catalytically inactive Cas proteins. Through fluorescence readout assays, we verified that the overexpression of cathepsin B in cancer cells can potentially be leveraged for novel therapeutic and biotechnological applications.
We overexpressed cathepsin B in HEK293T cells to investigate the cleavage of five different peptide linkers using our mCherry Expression Cassette (BBa_K5237022). To validate the functionality of the GFLG linker, we cloned it into a mammalian expression vector in between the Gal4 and VP64 domains (BBa_K5237020). Functional testing of this fusion protein demonstrated efficient cleavage of the GFLG linker by cathepsin B in vivo when cells were treated with doxorubicin, while other tested linkers showed no significant response.

1 Sequence Overview
2 Usage and Biology
3 Assembly and Part Evolution
4 Results
5 Conclusion
- 5.1 GFLG Is a Promising Candidate for Targeted Applications in Environments With Upregulated Cathepsin B Activity
- 5.2 Enabling the Functionalization of our PICasSO Toolbox Through Cathepsin B Cleavage
6 References

The PICasSO Toolbox

Figure 1: How Our Part Collection can be Used to Engineer New Staples

While synthetic biology has in the past focused on engineering the genomic sequence of organisms, the 3D spatial organization of DNA is well-known to be an important layer of information encoding in particular in eukaryotes, playing a crucial role in gene regulation and hence cell fate, disease development, evolution, and more. However, tools to precisely manipulate and control the genomic spatial architecture are limited, hampering the exploration of 3D genome engineering in synthetic biology. We - the iGEM Team Heidelberg 2024 - have developed PICasSO, a powerful molecular toolbox for rationally engineering genome 3D architectures in living cells, based on various DNA-binding proteins.

The PICasSO part collection offers a comprehensive, modular platform for precise manipulation and re-programming of DNA-DNA interactions using engineered "protein staples" in living cells. This enables researchers to recreate naturally occurring alterations of 3D genomic interactions, such as enhancer hijacking in cancer, or to design entirely new spatial architectures for artificial gene regulation and cell function control. Specifically, the fusion of two DNA binding proteins enables to artificially bring otherwise distant genomic loci into spatial proximity. To unlock the system's full potential, we introduce versatile chimeric CRISPR/Cas complexes, connected either at the protein or - in the case of CRISPR/Cas-based DNA binding moieties - the guide RNA level. These complexes are referred to as protein- or Cas staples, respectively. Beyond its versatility with regard to the staple constructs themselves, PICasSO includes robust assay systems to support the engineering, optimization, and testing of new staples in vitro and in vivo. Notably, the PICasSO toolbox was developed in a design-build-test-learn engineering cycle closely intertwining wet lab experiments and computational modeling and iterated several times, yielding a collection of well-functioning and -characterized parts.

At its heart, the PICasSO part collection consists of three categories.
(i) Our DNA-binding proteins include our finalized Cas staple experimentally validated using an artificial "enhancer hijacking" system as well as "half staples" that can be combined by scientists to compose entirely new Cas staples in the future. We also include our Simple staples comprised of particularly small, simple and robust DNA binding domains well-known to the synthetic biology community, which serve as controls for successful stapling and can be further engineered to create alternative, simpler, and more compact staples.
(ii) As functional elements, we list additional parts that enhance and expand the functionality of our Cas and Basic staples. These consist of staples dependent on cleavable peptide linkers targeted by cancer-specific proteases or inteins that allow condition-specific, dynamic stapling in vivo. We also include several engineered parts that enable the efficient delivery of PICasSO's constructs into target cells, including mammalian cells, with our new interkingdom conjugation system.
(iii) As the final category of our collection, we provide parts that underlie our custom readout systems. These include components of our established FRET-based proximity assay system, enabling users to confirm accurate stapling. Additionally, we offer a complementary, application-oriented testing system based on a luciferase reporter, which allows for straightforward experimental assessment of functional enhancer hijacking events in mammalian cells.

The following table gives a comprehensive overview of all parts in our PICasSO toolbox. The highlighted parts showed exceptional performance as described on our iGEM wiki and can serve as a reference. The other parts in the collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer their own custom Cas staples, enabling further optimization and innovation in the new field of 3D genome engineering.

Our part collection includes:

DNA-Binding Proteins: Modular building blocks for engineering of custom staples to mediate defined DNA-DNA interactions in vivo
BBa_K5237000	Fusion Guide RNA Entry Vector MbCas12a-SpCas9	Entry vector for simple fgRNA cloning via SapI
BBa_K5237001	Staple Subunit: dMbCas12a-Nucleoplasmin NLS	Staple subunit that can be combined with crRNA or fgRNA and dSpCas9 to form a functional staple
BBa_K5237002	Staple Subunit: SV40 NLS-dSpCas9-SV40 NLS	Staple subunit that can be combined with a sgRNA or fgRNA and dMbCas12a to form a functional staple
BBa_K5237003	Cas Staple: SV40 NLS-dMbCas12a-dSpCas9-Nucleoplasmin NLS	Functional Cas staple that can be combined with sgRNA and crRNA or fgRNA to bring two DNA strands into close proximity
BBa_K5237004	Staple Subunit: Oct1-DBD	Staple subunit that can be combined to form a functional staple, for example with TetR. Can also be combined with a fluorescent protein as part of the FRET proximity assay
BBa_K5237005	Staple Subunit: TetR	Staple subunit that can be combined to form a functional staple, for example with Oct1. Can also be combined with a fluorescent protein as part of the FRET proximity assay
BBa_K5237006	Simple Staple: TetR-Oct1	Functional staple that can be used to bring two DNA strands in close proximity
BBa_K5237007	Staple Subunit: GCN4	Staple subunit that can be combined to form a functional staple, for example with rGCN4
BBa_K5237008	Staple Subunit: rGCN4	Staple subunit that can be combined to form a functional staple, for example with rGCN4
BBa_K5237009	Mini Staple: bGCN4	Assembled staple with minimal size that can be further engineered
Functional Elements: Protease-cleavable peptide linkers and inteins are used to control and modify staples for further optimization for custom applications
BBa_K5237010	Cathepsin B-cleavable Linker: GFLG	Cathepsin B-cleavable peptide linker that can be used to combine two staple subunits to make responsive staples
BBa_K5237011	Cathepsin B Expression Cassette	Expression cassette for the overexpression of cathepsin B
BBa_K5237012	Caged NpuN Intein	A caged NpuN split intein fragment that undergoes protein trans-splicing after protease activation, which can be used to create functionalized staple subunits
BBa_K5237013	Caged NpuC Intein	A caged NpuC split intein fragment that undergoes protein trans-splicing after protease activation, which can be used to create functionalized staple subunits
BBa_K5237014	Fusion Guide RNA Processing Casette	Processing cassette to produce multiple fgRNAs from one transcript, that can be used for multiplexed 3D genome reprogramming
BBa_K5237015	Intimin anti-EGFR Nanobody	Interkingdom conjugation between bacteria and mammalian cells, as an alternative delivery tool for large constructs
BBa_K4643003	IncP Origin of Transfer	Origin of transfer that can be cloned into the plasmid vector and used for conjugation as a means of delivery
Readout Systems: FRET and enhancer recruitment readout systems to rapidly assess successful DNA stapling in bacterial and mammalian cells
BBa_K5237016	FRET-Donor: mNeonGreen-Oct1	FRET donor-fluorophore fused to Oct1-DBD that binds to the Oct1 binding cassette, which can be used to visualize DNA-DNA proximity
BBa_K5237017	FRET-Acceptor: TetR-mScarlet-I	Acceptor part for the FRET assay binding the TetR binding cassette, which can be used to visualize DNA-DNA proximity
BBa_K5237018	Oct1 Binding Casette	DNA sequence containing 12 Oct1 binding motifs, compatible with various assays such as the FRET proximity assay
BBa_K5237019	TetR Binding Cassette	DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET proximity assay
BBa_K5237020	Cathepsin B-Cleavable Trans-Activator: NLS-Gal4-GFLG-VP64	Readout system that responds to protease activity, which was used to test cathepsin B-cleavable linker
BBa_K5237021	NLS-Gal4-VP64	Trans-activating enhancer, that can be used to simulate enhancer hijacking
BBa_K5237022	mCherry Expression Cassette: UAS, minimal Promoter, mCherry	Readout system for enhancer binding, which was used to test cathepsin B-cleavable linker
BBa_K5237023	Oct1 - 5x UAS Binding Casette	Oct1 and UAS binding cassette, that was used for the simulated enhancer hijacking assay
BBa_K5237024	TRE-minimal Promoter- Firefly Luciferase	Contains firefly luciferase controlled by a minimal promoter, which was used as a luminescence readout for simulated enhancer hijacking

1. Sequence Overview

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

2. Usage and Biology

Figure 2: Cathepsin B Cleavage Sites in the GFLG Peptide Linker.

Cathepsin B is a cysteine protease that is significantly overexpressed in various cancer types, including breast and colorectal cancer (Ruan et al., 2015). Proteolytic cleavage of pro-biologics, for example through cathepsin B activity, allows for precise temporal and spatial regulation of biopharmaceutical activity in therapeutic strategies (Bleuez et al., 2022).
In this context, we introduce the cathepsin B-cleavable peptide linker GFLG as a functional addition to our PICasSO toolbox, enabling a wide range of therapeutic and synthetic biology applications. GFLG has been shown to be cleaved by cathepsin B (Wang et al., 2024), with cleavage occurring either between the phenylalanine and leucine or after the second glycine of the linker (Rejmanová et al., 1983; see Fig. 2).
Through a fluorescence readout assay in HEK293T cells, we identified GFLG as the most effective among five peptide linkers known to be cleaved by cathepsin B (Jin et al., 2022; Shim et al., 2022; Wang et al., 2024). This linker could facilitate cleavage-induced oligomerisation of Cas proteins via protein trans-splicing of caged intein fragments (BBa_K5237012, BBa_K5237013), further enhancing the capabilities of our system.

3. Assembly and Part Evolution

3.1 Implementation of a Cleavage-Responsive Fluorescence Readout Assay

We designed a fluorescence readout assay in HEK293T cells based on expression of mCherry induced by the trans-activator VP64. VP64 was conjugated to the DNA-binding domain (DBD) of Gal4 through the GFLG linker. We purchased the nucleotide sequence encoding the GFLG linker as an oligo. After annealing the oligo, we cloned it into a mammalian expression vector between the open reading frames for Gal4-DBD and VP64 via Golden Gate assembly (BBa_K5237020). Binding of Gal4-DBD upstream of a gene encoding the fluorescence protein mCherry induces overexpression of mCherry by VP64. Consequently, separation of Gal4-DBD and VP64 by cathepsin B cleavage of the GFLG linker reduces mCherry expression (Fig. 3).

Figure 3: Schematic Illustration of the Cathepsin B Fluorescence Readout Assay. The DNA-binding domain (DBD) of Gal4 is conjugated to the transactivator domain VP64 via a cathepsin B-cleavable peptide linker. Binding of the Gal4-DBD to the upstream activating sequence (UAS) in proximity to the mCherry gene induces mCherry overexpression via VP64. Cathepsin B cleavage of the linker separates Gal4-DBD and VP64 and consequently reduces mCherry expression.

We transfected our genetic constructs into HEK293T cells. The transfected plasmids encoded mCherry, the Gal4-VP64 constructs with different linkers, and cathepsin B (Fig. 4). Additionally, a stuffer plasmid and a plasmid encoding eGFP were transfected for normalization. The negative control was not transfected with the plasmid encoding cathepsin B. We investigated two different test conditions, in which we either transfected 30 ng or 60 ng of the plasmid encoding cathepsin B. The fluorescence intensity of mCherry was measured 48 hours after transfection. Our initial tests did not result in the unambiguous identification of a cathepsin B-cleavable peptide linker (Fig. 5). For all linkers, we did not observe a large decrease in fluorescence intensity between the negative control and test conditions. In some conditions, the fluorescence intensity even increased between the negative control and test conditions.

Figure 4: Transfection Plan of HEK293T Cells for Fluorescence Readout Experiments. HEK293T cells in a 96-well plate were transfected with plasmids encoding mCherry, the Gal4-VP64 constructs with different linkers, and cathepsin B (CatB). Additionally, a stuffer plasmid and a plasmid encoding eGFP were transfected for normalization.

Figure 5: Fluorescence Readout After 48 Hours for Five Different Peptide Linkers and Three Different Conditions. The fluorescence intensity for mCherry was measured for five different linkers. The negative control was not transfected with the plasmid encoding cathepsin B. The fluorescence intensity of the negative control was set to one. Two different test conditions were investigated, in which either 30 ng or 60 ng of the plasmid encoding cathepsin B were transfected.

3.2 Changes to the Amino Acid Sequence of Cathepsin B Did Not Improve Cleavage Efficiency

Since cathepsin B is a lysosomal protease that is normally only active in the lysosome and the extracellular environment but not in the cytosol, we decided to change the native amino acid sequence of cathepsin B. Upon further investigation of the lysosomal maturation process of cathepsin B, we chose to express a truncated and mutated version of cathepsin B. We truncated the native cathepsin B amino acid sequence N-terminally by the first twenty amino acids. This N-terminally truncated version of cathepsin B lacks a signal peptide that normally facilitates translation of cathepsin B in the rough endoplasmic reticulum. Additionally, truncation of the first twenty amino acids of cathepsin B had previously been observed to maintain catalytic activity even in the absence of lysosomal proteases like pepsin (Müntener et al., 2005). Additionally, we introduced three point mutations (D22A, H110A, R116A) in the amino acid sequence of cathepsin B. This has been shown to increase the activity of cathepsin B at higher pH values by disrupting the interactions of an occluding loop with the substrate binding pocket of cathepsin B (Nägler et al., 1997).
We performed the same fluorescence readout assay in HEK293T cells that we also used for wild-type cathepsin B. The fluorescence intensity of mCherry was measured 48 hours after transfection. However, we observed no decrease in fluorescence between our negative control and test conditions, indicating that Gal4-DBD-Linker-VP64 was not cleaved (Fig. 6). Additionally, we performed a western blot, where the bands for the truncated and mutated version of cathepsin B were barely visible or absent altogether, indicating lower protein expression compared to the wild type (Fig. 7). Another key insight from this experiment was that this version of cathepsin B was not activated by cleavage in the cell, as no additional protein bands were observed.

Figure 6: Fluorescence Readout for the Truncated and Mutated Version of Cathepsin B. Fluorescence intensity for mCherry was measured across five different linkers. The negative control, which was not transfected with the plasmid encoding cathepsin B, was assigned a fluorescence intensity value of one. Two test conditions were explored, where either 30 ng or 60 ng of the plasmid encoding cathepsin B was transfected.

3.3 Doxorubicin Induces Lysosomal Escape of Cathepsin B

Since our truncated and mutated version of cathepsin B did not seem to be active in the cytosol, we decided to go back to wild-type cathepsin B. Therefore, we focused on improving the activity of wild-type cathepsin B in the cytosol. After consulting the literature, we decided to treat cells with the cytostatic doxorubicin to induce lysosomal escape of cathepsin B, as had been previously reported (Bien et al., 2004).

4. Results

4.1 Mature Cathepsin B Is Expressed in HEK293T Cells

To achieve cathepsin B cleavage-induced Cas stapling, catalytically active cathepsin B needs to be expressed in the cytosol. Therefore, we investigated the expression of different cathepsin B constructs under different conditions in HEK293T cells. In addition to wild-type (wt) cathepsin B, we also cloned a truncated and mutated version of cathepsin B (Δ1-20, D22A, H110A, R116A) and compared protein expression of both constructs in doxorubicin-treated and untreated conditions.
Figure 7 shows a western blot of the wt version of cathepsin B as well as the truncated and mutated version of cathepsin B (Δ1-20, D22A, H110A, R116A). Cells of both cathepsin B versions were treated with 500 nM doxorubicin (dox) 24 hours post-transfection and incubated for additional 24 hours. For each condition, three replicates were blotted. We observed no differences in protein expression levels between the dox-treated and untreated wt versions of cathepsin B. For the truncated and mutated version of cathepsin B, however, only the untreated samples showed the corresponding band at approximately 36 kDa expected for this version of cathepsin B. Additionally, the bands of the truncated and mutated version appeared much weaker than the ones of the wt, indicating poorer protein expression. The household protein β-tubulin is visible in all samples at approximately 55 kDa. The wt cathepsin B additionally showed bands for pro-cathepsin B at approximately 42 kDa, a mature single-chain version of cathepsin B at approximately 33 kDa and a mature double-chain version at approximately 26 kDa.

Figure 7: Western Blot of Two Versions of Cathepsin B With and Without Doxorubicin. From left to right: protein ladder, wild-type (wt) cathepsin B with (+) and without (-) doxorubicin, truncated and mutated version of cathepsin B with (+) and without (-) doxorubicin. The household protein β-tubulin is visible in all samples at 55 kDa. The wt cathepsin B also shows bands for pro-cathepsin B at 42 kDa, mature single-chain cathepsin B at 33 kDa and mature double-chain cathepsin B at 26 kDa. The band for the truncated and mutated version of cathepsin B can be seen in the samples without doxorubicin at 36 kDa.

4.2 mCherry and eGFP Can be Used as a Reporter System to Measure Cleavage Efficiency

In this experiment, mCherry and eGFP were evaluated as reporters to quantify the efficiency of cathepsin B-mediated cleavage of Gal4-Linker-VP64 constructs in HEK293T cells.
Figure 8 shows micrographs taken with a fluorescence microscope of three different conditions: the null control, the negative control and the test sample. Figure 9shows the corresponding graphs quantifying the fluorescence intensity in the different conditions. All samples were transfected with plasmids encoding eGFP and mCherry. The null control and the negative control were not transfected with the plasmid encoding cathepsin B. The null control was also not transfected with any of the plasmids encoding Gal4-Linker-VP64 constructs. The test sample was transfected with 30 ng of the plasmid encoding cathepsin B and with the plasmid encoding Gal4-GFLG-VP64. As expected, the null control showed no detectable mCherry signal, since no plasmid encoding a Gal4-V64 construct was transfected. Consequently, mCherry overexpression via VP64 could not be induced. However, we observed a high fluorescence intensity for eGFP, indicating that the transfection was successful. The negative control showed strong signals of both mCherry and eGFP. Therefore, it can be assumed that the transfection was successful and that our mCherry readout system is functional. Interestingly, there are some cells which either seem to only express mCherry or eGFP and some cells that show no fluorescence signal. The test sample showed less eGFP and mCherry fluorescence compared to the negative control. We expected to observe reduced fluorescence intensity of mCherry, as the transfected cells would express cathepsin B, which cleaves the linker, thereby decreasing mCherry expression.

Figure 8: Micrographs of HEK293T Cells in Two Control Conditions and One Test Condition. Micrographs were taken with a fluorescence microscope 48 hours after transfection. An overlay of brightfield, eGFP and mCherry is shown. The null control and the negative control were not transfected with the plasmid encoding cathepsin B. The Null Control was also not transfected with any of the plasmids encoding Gal4-Linker-VP64 constructs. The test sample was transfected with 30 ng of the plasmid encoding cathepsin B and with the plasmid encoding Gal4-GFLG-VP64. The micrograph of the test sample is not from the same biological replicate as the micrographs of the two controls.

Figure 9: Fluorescence Readout After 48 Hours for Two Control Conditions and One Test Condition. The fluorescence intensity for mCherry was measured for the GFLG linker and normalized against a baseline eGFP fluorescence intensity. The null control and the negative control were not transfected with the plasmid encoding cathepsin B. The null control was also not transfected with any of the plasmids encoding Gal4-Linker-VP64 constructs. The test sample was transfected with 30 ng of the plasmid encoding cathepsin B and with the plasmid encoding Gal4-GFLG-VP64.

4.3 The Peptide Linker GFLG Is Cleaved by Cathepsin B in Vivo

We performed a fluorescence readout assay in HEK293T cells to investigate cathepsin B cleavage of different peptide linkers. 24 hours after transfection, we added doxorubicin in a final concentration of 500 nM to the cell supernatant. Figure 10 shows the fluorescence intensity of mCherry for five different peptide linkers (GFLG, FFRG, FRRL, VA, FK). The negative control was not transfected with the plasmid encoding cathepsin B. We investigated two different test conditions, in which we either transfected 30 ng or 60 ng of the plasmid encoding cathepsin B. The fluorescence intensity of mCherry was normalized by the measured fluorescence intensity of eGFP in each condition. Additionally, the values for 30 ng and 60 ng cathepsin B were normalized against the corresponding negative controls. One data point for the VA linker, transfected with 60 ng of the plasmid encoding cathepsin B, was excluded due to severe deviation from the other values. We conducted a two-way analysis of variance (ANOVA) to assess the significance of the observed differences between the negative control and the test conditions for each linker. As the negative control did not contain the plasmid encoding cathepsin B, we expected the measured fluorescence intensity of mCherry to be the highest in these conditions. However, this was only observed for the GFLG and FK linkers. Contrary to our expectations, the fluorescence intensity of the negative control was the lowest out of the three conditions tested for the remaining linkers. It appears that the addition of the plasmid encoding cathepsin B increases mCherry fluorescence intensity when the linker is not cleaved. However, this increase is only significant for the FFRG linker in the 60 ng condition. For the GFLG linker, we observed significant decreases in fluorescence intensity between the negative control and both test conditions, with no difference between the 30 ng and 60 ng conditions. For the FK linker, no significant decreases in fluorescence intensity between the negative control and the test conditions were observed.

Figure 10: Fluorescence Readout After 48 Hours for Five Different Peptide Linkers and Three Different Conditions. The fluorescence intensity for mCherry was measured for five different linkers and normalized against a baseline eGFP fluorescence intensity. The negative control was not transfected with the plasmid encoding cathepsin B. The fluorescence intensity of the negative control was set to one. Two different test conditions were investigated, in which either 30 ng or 60 ng of the plasmid encoding cathepsin B were transfected. The fluorescence readout was analyzed using a two-way ANOVA. Medium: DMEM (10% FCS). P values: ns, P > 0.05; *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.

5. Conclusion

5.1 GFLG Is a Promising Candidate for Targeted Applications in Environments With Upregulated Cathepsin B Activity

All in all, these findings demonstrate that our fluorescence-based readout assay reliably detects cathepsin B-mediated cleavage of peptide linkers, with the GFLG linker showing particularly high susceptibility to enzymatic cleavage. This makes GFLG a promising candidate for targeted applications in environments with elevated cathepsin B activity, such as cancerous tissues.
Additionally, our assay can be used to identify other cathepsin B-cleavable peptide linkers or improve our current GFLG linker. Our assay can also be adapted for other proteases, such as different caspases involved in neurodegenerative conditions (Espinosa-Oliva et al., 2019).

5.2 Enabling the Functionalization of our PICasSO Toolbox Through Cathepsin B Cleavage

Our GFLG linker can be combined with caged inteins (Gramespacher et al., 2017) conjugated to catalytically dead Cas9, allowing for selective induction of Cas-stapling in the presence of cathepsin B. This enables the functionalization of our PICasSO toolbox for in vitro and in vivo applications.
This innovative approach paves the way for new strategies in precision medicine and synthetic biology, offering the potential for targeted therapeutic interventions.

6. References

Bien, S., Ritter, C. A., Gratz, M., Sperker, B., Sonnemann, J., Beck, J. F., Kroemer, H. K. (2004). Nuclear factor-kappaB mediates up-regulation of cathepsin B by doxorubicin in tumor cells. Molecular Pharmacology 65(5), 1092-102. https://doi.org/10.1124/mol.65.5.1092

Bleuez, C., Koch, W. F., Urbach, C., Hollfelder, F., & Jermutus, L. (2022). Exploiting protease activation for therapy. Drug Discov Today, 27(6), 1743-1754. https://doi.org/10.1016/j.drudis.2022.03.011

Espinosa-Oliva, A. M., García-Revilla, J., Alonso-Bellido, I. M., & Burguillos, M. A. (2019). Brainiac Caspases: Beyond the Wall of Apoptosis [Mini Review]. Frontiers in Cellular Neuroscience, 13. https://doi.org/10.3389/fncel.2019.00500

Gramespacher, J. A., Stevens, A. J., Nguyen, D. P., Chin, J. W., & Muir, T. W. (2017). Intein Zymogens: Conditional Assembly and Splicing of Split Inteins via Targeted Proteolysis. J Am Chem Soc, 139(24), 8074-8077. https://doi.org/10.1021/jacs.7b02618

Jin, C., EI-Sagheer, A. H., Li, S., Vallis, K. A., Tan, W., & Brown, T. (2022). Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers. Angewandte Chemie International Edition, 61(13), e202114016. https://doi.org/10.1002/anie.202114016

Müntener, K., Willimann, A., Zwicky, R., Svoboda, B., Mach, L., & Baici, A. (2005). Folding Competence of N-terminally Truncated Forms of Human Procathepsin B*. Journal of Biological Chemistry, 280(12), 11973-11980. https://doi.org/10.1074/jbc.M413052200

Nägler, D. K., Storer, A. C., Portaro, F. C. V., Carmona, E., Juliano, L., & Ménard, R. (1997). Major Increase in Endopeptidase Activity of Human Cathepsin B upon Removal of Occluding Loop Contacts. Biochemistry, 36(41), 12608-12615. https://doi.org/10.1021/bi971264+

Rejmanová, P., Kopeček, J., Pohl, J., Baudyš, M., & Kostka, V. (1983). Polymers containing enzymatically degradable bonds, 8. Degradation of oligopeptide sequences in N-(2-hydroxypropyl)methacrylamide copolymers by bovine spleen cathepsin B. Die Makromolekulare Chemie, 184(10), 2009-2020. https://doi.org/10.1002/macp.1983.021841006

Ruan, H., Hao, S., Young, P., & Zhang, H. (2015). Targeting Cathepsin B for Cancer Therapies. Horiz Cancer Res, 56, 23-40.

Shim, N., Jeon, S. I., Yang, S., Park, J. Y., Jo, M., Kim, J., Choi, J., Yun, W. S., Kim, J., Lee, Y., Shim, M. K., Kim, Y., & Kim, K. (2022). Comparative study of cathepsin B-cleavable linkers for the optimal design of cathepsin B-specific doxorubicin prodrug nanoparticles for targeted cancer therapy. Biomaterials, 289, 121806. https://doi.org/10.1016/j.biomaterials.2022.121806

Wang, J., Liu, M., Zhang, X., Wang, X., Xiong, M., & Luo, D. (2024). Stimuli-responsive linkers and their application in molecular imaging. Exploration, 4(4), 20230027. https://doi.org/10.1002/EXP.20230027

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