12 Types of Targeted Protein Degradation Technologies.pdf

Biopharma PEG https://www.biochempeg.com
12 Types of Targeted Protein Degradation
Technologies
Since the first PROTAC molecule entered clinical development in March 2019, Targeted
Protein Degradation (TPD) technology has developed rapidly. On the one hand, several
PROTAC and molecular glues have entered clinical trials worldwide, and some leading
projects have disclosed clinical investigation data several times; on the other hand, new
technologies have emerged, such as LYTAC, ATTEC, ATAC, AUTOTAC, etc. In this
article, we list the targeted protein degradation technologies that have made
important research progress in recent years, mainly including mechanism of action,
representative companies, global R&D status, etc.
Figure 1. Representative events in the TPD development. Image source: reference [1]
Targeted protein degradation via proteasome
Protein homeostasis refers to the highly complex and interrelated processes that cells use
to maintain protein concentration, conformation and subcellular localization. It consists of
a series of pathways that control protein synthesis, folding, transport, and disposal. In
eukaryotic cells, damaged proteins or organelles are able to be cleared by

the proteasome or lysosome. These two pathways are independent but interconnected
with each other. In general, the proteasome eliminates short-lived proteins and soluble
misfolded proteins through the ubiquitin-proteasome system (UPS). In contrast,
lysosomes are responsible for the degradation of long-lived proteins, insoluble protein
aggregates, and even whole organelles, macromolecular compounds, and intracellular
parasites (e.g., certain bacteria) via the endocytosis, phagocytosis, or autophagy
pathways. First, we present targeted protein degraders (TPDs) developed based on
proteasomes.
Figure 2. Different TPD technologies, source: reference [1]
PROTAC (Proteolysis-Targeting Chimeras)
PROTACs, known as Proteolysis-Targeting Chimeras, are heterobifunctional molecules
consisting of an E3 ligase binder, a Linker, and a target protein binder. Specifically, one
end of the PROTACs molecule is bound to the target protein and the other end is bound to
the E3 ubiquitin ligase. The E3 ubiquitin ligase marks the target protein as defective or
damaged by attaching a small protein called ubiquitin to it. Afterward, the proteasome
degrades the tagged target protein.
By the way, PROTAC linker plays a vital role in the efficient ubiquitination of the target
protein and its ultimate degradation. PEG linkers are the most common motifs
incorporated into PROTAC linker structures. Biopharma PEG is dedicated to the R&D

of PROTAC Linker, providing high purity PEG linkers with various reactive groups
to continuously assist your project development.
Figure 3. PROTAC Global R&D Overview and Hot Targets, source: reference [2]
PROTAC has been in development for more than 20 years. According to statistics, there
are currently over 160 PROTAC projects in development worldwide, and nearly 20
projects are already in clinical development, with companies in the first tier
including Arvinas, Kymera, C4 Therapeutics, Nurix Therapeutics, Haisco Pharmaceutical,
Kintor Pharma-B, BeiGene, etc. Currently, the more competitive targets include AR, BTK,
BET, ALK, EGFR, etc.

Figure 4. PROTACs in Pipeline
Molecular Glue
Molecular glue degraders are a class of small molecules that induce novel interactions
between E3 ubiquitin ligase substrate receptors and target proteins, leading to the
degradation of the target protein. A notable example of molecular glue is the thalidomide
anticancer drugs, which redirect the E3 ubiquitin ligase CRL4CRBN, thereby
polyubiquitinating the transcription factors IKZF1 and IKZF3, leading to the degradation of
IKZF1 and IKZF3 by the proteasome. Similarly, the anticancer sulfonamide drug indisulam

directs the E3 ubiquitin ligase CRL4DCAF15 to degrade the splicing factors RBM23 and
RBM39.
Figure 5. Molecular Glues vs PROTACs
Although both molecular glues and PROTACs utilize UPS for protein degradation,
they differ in several ways. First, PROTAC is a heterobifunctional degradant that
interacts with both E3 ligase and protein of interest (POI), compared to molecular glue
degraders that can only interact with E3 ligase (more frequently) or POI and then
induce/stabilize E3 ligase interaction with POI. Second, compared to PROTACs,
molecular glues do not contain a linker and therefore have a smaller molecular weight,
higher oral bioavailability, and better cell permeability. Finally, although rational design
strategies are emerging, molecular glues are currently more difficult to design.
Examples of molecular glue degraders include thalidomide, lenalidomide, and
pomalidomide. Interestingly, they have been approved by the FDA for the treatment of
various types of tumors long before their functional mechanisms were elucidated.

Although the research and development of molecular glues have not yet formed the same
scale as PROTAC, several companies around the world have joined the research and
development, and the fastest progressing projects are in Phase I/II clinical, with
representative startups such as Monte Rosa Therapeutics and Gluetacs Therapeutics,
etc.
It is worth mentioning that in 2022, the financing fever in the molecular glue field has
increased, with several companies dedicated to molecular glue development announcing
financing, such as Plexium, TRIANA Biomedicines, Ambagon Therapeutics, etc.; in
addition, pharmaceutical giants such as BMS and Merck have announced large molecular
glue-related collaborations. It is expected that the molecular glue field will receive more
support in the coming years.
CHAMP (Chaperone-mediated Protein Degradation/Degrader)
Chaperones are involved in the folding of more than half of all mammalian proteins.
Chaperones contain many different families, such as the HSP60 family, the HSP70 family,
and the HSP90 family, each of which helps protein folding in a different way.
In addition to participating in protein folding, in some cases, chaperones can also
recognize misfolded proteins and guide them through the ubiquitin-proteasome system
(UPS) for degradation. Some chaperones, such as heat shock protein 90 (HSP90),
interact directly with many different E3 ubiquitin ligases, thereby assisting in the
completion of protein degradation and preventing the normal localization of misfolded
proteins by preventing them from interfering with normal cellular function.

Figure 6. CHAMP (Chaperone-mediated Protein Degradation/Degrader), source: Ranok
Therapeutics
It was found that the HSP90 complex is highly activated in tumor tissues relative to normal
tissues, which leads to small molecule compounds that bind HSP90 to display unique
tumor-selective pharmacokinetics.
Using these properties of HSP90, Ranok Therapeutics developed a heterobifunctional
small molecule that targets both BRD4 and HSP90, also known as CHAMP. In January
2022, the US FDA has approved the IND application for RNK05047, a small molecule
BRD4 selective degradation agent, and patient enrollment for Phase I/II clinical trials is
expected to begin in the first half of 2022.
Targeted protein degradation via lysosome
In cells, three different lysosomal pathways allow protein degradation: 1) cell surface
proteins reach the lysosome via endocytosis, after which they can be degraded by the
lysosome or transported to the plasma membrane or other organelles for recycling. 2) in
the phagocytic pathway, cells phagocytose large extracellular particles, such as invading
pathogens and dead cells, which are then degraded via the lysosome. 3) Misfolded or
aggregated proteins, damaged organelles, and intracellular pathogens are removed via

the autophagy-lysosome pathway. Among them, there are three different forms of
autophagy, including macroautophagy, microautophagy, and chaperone-mediated
autophagy (CMA).
Figure 7. Protein degradation via three distinct lysosome pathways. source: reference [1]
In macroautophagy, dysfunctional proteins or organelles are recognized by autophagic
receptors and selectively enclosed in autophagosomes, after which the autophagosomes
fuse with lysosomes and their contents are degraded. In microautophagy, the lysosome
directly swallows the autophagic cargo and causes its degradation. In CMA, chaperones
select target proteins and directly span the lysosomal membrane for degradation. there
are two unique features of CMA: first, CMA only degrades certain proteins and not
organelles; second, autophagosome formation is not necessary in CMA.

Figure 8. Summary of lysosome-dependent protein degradation strategies. source:
reference [1]
With the in-depth study of different lysosomal degradation pathways, scientists have
developed a variety of novel protein degradation techniques, including LYTAC, ATAC,
AbTAC, GlueTAC, AUTAC, ATTEC, AUTOTAC, etc. It is worth mentioning that compared
to proteasome-based targeted protein degradation technologies that can only degrade
certain intracellular proteins, lysosome-based targeted protein degradation technologies
have the potential to remove protein aggregates, damaged excess organelles, membrane
proteins and extracellular proteins, and therefore, the clinical development of these
technologies is highly anticipated.
LYTAC (Lysosome-Targeting Chimaeras）

LYTAC, similar to PROTAC, is a bifunctional molecule with two binding domains (below),
one end carrying an oligoglycopeptide moiety that binds to the cell surface
transmembrane receptor CI-M6PR (cation-independentmannose-6-phosphatereceptor),
and the other end carries an antibody or small molecule that binds to the target protein.
These two binding domains are linked by a chemical linker. The trimeric
CI-M6PR-LYTAC-target protein complex formed on the plasma membrane is "engulfed"
by the cell membrane and forms a transport vesicle. The vesicle transports the complex to
the lysosome, where the target protein is degraded.
Figure 9. The mechanism of LYTAC, source: reference [3]

Unlike PROTAC (which degrades intracellular proteins), LYTAC is mainly used to degrade
extracellular and membrane-bound proteins. As many therapeutic targets (e.g. growth
factors, disease-associated receptors, cytokines) actually belong to secreted
(extracellular) and membrane-associated proteins, the LYTAC technology has a very
promising therapeutic future as an effective tool capable of expanding the range of
degradable proteins.
A representative company developing LYTAC is Lycia Therapeutics, a San
Francisco-based company founded in 2019 and driven by Versant Ventures, which has
raised $120 million in cumulative funding. In August 2021, Lycia announced a multi-year
research collaboration and licensing agreement with pharmaceutical giant Eli Lilly, under
which the two companies will utilize Lycia's proprietary LYTAC technology to develop and
commercialize novel degradation agents against up to five targets, with a focus on
disease areas including immunity and pain. Under the terms of the agreement, Lycia will
receive an upfront payment of $35 million, in addition to being eligible for more than $1.6
billion in potential milestone payments and a share of future sales. At this time, Lycia has
not disclosed any pipeline and is looking forward to specific projects to be announced in
2022.
ATAC (ASGPR Targeting Chimeras)
ATAC is known as ASGPR Targeting Chimeras, or a sialoglycoprotein receptor (ASGPR)
targeting chimera, an endocytic surface receptor that plays a key role in the natural
process by which endogenous proteins are internalized into hepatocytes and degraded.
Figure 10. ASGPR Targeting Chimeras, source: Avilar

Overall, ATAC is similar to LYTAC and acts as a bifunctional molecule, binding to the
target protein on one end and to ASGPR on the other. The resulting ASGPR-ATAC-target
protein complex is "engulfed" by the cell membrane, forming a transport vesicle, which
transports the complex to the hepatocyte lysosome, where the target protein is degraded.
Since ASGPR is a liver-specific lysosomal targeting receptor, the ATAC technology has a
potential safety advantage over LYTAC (CI-M6PR is widely expressed in a variety of cells)
in that it can degrade extracellular proteins in a cell-type restricted manner.
The company that came up with the ATAC concept, called Avilar Therapeutics,
announced in November 2021 that it had received $60 million in seed funding from
founding investor RA Capital Management. Avilar's goal is to target disease-causing
extracellular proteins and broaden the target boundaries of protein degraders.
It is worth mentioning that technologies such as GalNAc-LYTAC (developed by the team
of LYTAC pioneer Prof. Carolyn R. Bertozzi) and MoDE-A have the same mechanism as
ATAC and are named differently by different research teams. Based on the design ideas
of LYTAC and ATAC, it is worth looking forward to whether scientists can develop new
degradation technologies based on other lysosomal targeting receptors in the future.
Figure 11. GalNAc-LYTAC and MoDE-A, source: reference [4]

BIAC (Bispecific Aptamer Chimera)
The mechanism of action of bispecific aptamer chimeras is similar to that of LYTAC,
mediating POI degradation via the nucleosome-lysosome pathway. The difference is that
bispecific aptamer chimeras use DNA aptamers to target CI-MPR and transmembrane
POI. In February 2021, researchers from Shanghai Jiao Tong University and other
institutions designed the first bispecific aptamer chimera molecule, named A1-L-A2,
where A1 and A2 specifically bind the CI-MPR and a POI, and L stands for linker DNA. it
was shown that A1-L-A2 can transport membrane proteins, such as the receptor tyrosine
kinases MET and PTK-7, to the lysosome for degradation. transported to the lysosome for
degradation. At the same time, this aptamer chimera had no significant effect on the level
of non-targeted proteins. Compared with antibodies, nucleic acid aptamers have the
advantages of simple preparation, precise synthesis, and good stability, and are therefore
a promising class of technologies.
Figure 12. Bispecific Aptamer Chimera, source: reference [5]
AbTAC (Antibody-based PROTAC)
In a study published in January 2021 in the Journal of the American Chemical Society, a
team of scientists from the University of California, San Francisco proposed the

antibody-based PROTAC (AbTAC) technology. AbTAC, essentially a bispecific antibody,
recruits membrane-bound E3 ligases to degrade cell surface proteins. AbTAC has been
shown to degrade PD-L1 by recruiting the membrane-bound E3 ligase RNF43
(transmembrane E3 ligase).
Figure 13. Antibody-based PROTAC, source: reference [1]
Although the name is related to PROTAC, AbTAC is actually more similar to LYTAC
because both are based on the endosomal-lysosomal pathway to induce cell surface POI
degradation. AbTAC connects RNF43 on one end and POI on the cell surface on the
other, forming a complex that is internalized into the cell, after which POI is degraded by
the lysosome. However, the mechanism of action of AbTAC is not as clear as that of
LYTAC. For example, it is not clear whether the intracellular region of POI is ubiquitinated
prior to endocytosis; if so, the contribution of ubiquitination to the internalization of the
complex is yet to be investigated. In addition, whether RNF43 can be recycled and reused
like the receptors CI-MPR and ASGPR of LYTAC/ATAC needs to be further investigated.
In the future, AbTAC technology may need to work on finding other membrane receptors
for better development.
GlueTAC
GlueTAC is another lysosome-based degradation strategy developed to degrade cell
surface proteins and consists of a covalently modified single-domain antibody (nanobody),

a cell-penetrating peptide (CPP) and a lysosome-sorting sequence. The single-domain
antibody (nanobody) is responsible for targeting POI, CPP-induced endocytosis of the
GlueTAC-POI complex and subsequent lysosomal degradation.
Figure 14. GlueTAC, source: reference [1]
The collaborative team of Peng Chen and Jian Lin from the School of Chemical and
Molecular Engineering, Peking University, published research results related to GlueTAC
technology in the Journal of the American Chemical Society in October 2021. The study
developed a GlueTAC molecule that targets PD-L1 and demonstrated that compared to
the PD-L1 antibody atezolizumab, the GlueTAC molecule was more effective in reducing
PD-L1 levels in cells and inhibiting tumor growth in immunodeficient mice. Although
GlueTAC represents another exciting approach to degrade cell surface proteins, there are
still some issues to think about, such as safety, half-life, etc.
AUTAC (Autophagy-Targeting Chimera)

In addition to the nucleosomal-lysosomal pathway, the autophagosomal-lysosomal
pathway has also been used for the development of targeted protein degraders. The
nucleotide 8-nitro-cGMP (8-nitrocyclic guanosine monophosphate) is an important
signaling molecule for intracellular regulation of autophagosome recruitment. this property
of 8-nitro-cGMP has been used for the development of autophagy-targeting chimeras
(AUTAC). the AUTAC molecule consists of three components: a cGMP-based
degradation tag, a linker, and a small molecule ligand for a protein of interest (POI) or
organelle. AUTAC molecules trigger K63-linked polyubiquitination and subsequent
lysosome-mediated degradation. In contrast, PROTAC molecules induce K48-linked
polyubiquitination and proteasome-mediated degradation.
Figure 15. Autophagy-Targeting Chimera, source: reference [6]
In addition to cytoplasmic proteins, organelles such as mitochondria can also be degraded
by AUTAC. Mitochondrial dysfunction is associated with many aging-related diseases,

and removal of dysfunctional or damaged mitochondria can ameliorate these diseases. In
a study published in Molecular Cell in December 2019, a team of scientists developed an
AUTAC4 molecule that promotes fragmented mitochondrial autophagy. AUTAC4 uses
2-phenylindole derivatives, transporter ligands on the outer mitochondrial membrane, as
mitochondrial binder. These results suggest that AUTAC has a wide range of applications
and is expected to play a greater role in the degradation of protein aggregates, among
others.
ATTEC (Autophagosome-Tethering Compound)
Similar to the autophagy-based AUTAC technology, ATTEC works by binding POI to the
autophagosome. Specifically, ATTEC binds to both LC3, a key protein of
autophagosomes, and POI. During autophagy, the key protein LC3 is lipidated and then
polymerized and amplified to form a membrane structure, and wraps proteins, lipids,
organelles and other degradation targets in it to form a complete autophagosome, which
is fused with lysosomes to degrade the substances wrapped in it.
Figure 16. Autophagosome-Tethering Compound, source: reference [1]

In a study published in Nature in October 2019, Professor Lu Boxun's team at Fudan
University developed an ATTEC molecule that binds to both LC3 and mutant Huntington
protein (mHTT), thereby binding the target protein to autophagic vesicles for degradation.
In 2021 another paper published in the journal Cell Research paper confirmed that
ATTEC technology is also able to degrade lipid droplets, an intracellular organelle that
stores fat (excessive storage of lipid droplets may be associated with a variety of diseases,
such as obesity, NAFLD, neurodegenerative diseases, etc.), achieving a breakthrough in
targeted degradation technology from protein to non-protein substances.
Based on ATTEC technology, a company called PAQ Therapeutics has been formed with
Professor Lu Boxun as one of the co-founders. In July 2021, PAQ Therapeutics closed a
$30 million Series A round of funding. The company is initially focused on developing
therapeutics for inherited central nervous system diseases, with subsequent plans to
expand to other protein and non-protein targets for the treatment of oncology, metabolic
diseases, and other major diseases.
ATUOTAC (Autophagy-Targeting Chimera)
The autophagic cargo receptor p62/SQSTM1 acts as a bridge between polyubiquitinated
cargoes and autophagosomes. The polyubiquitinated cargo binds to the UBA structural
domain of p62, leading to a conformational change in p62. This conformational change
exposes the LIR motif of p62 and facilitates its interaction with LC3 at the autophagic
membrane.In February 2022, a paper published in Nature Communications by a team of
scientists from South Korea proposed the AUTOTAC technology. The AUTOTAC
molecule consists of a module that interacts with the ZZ domain of p62 and a
POI-targeting module. AUTOTAC acts to link POI and p62 independent of POI
ubiquitination. AUTOTAC promotes the oligomerization and activation of p62, leading to
POI degradation via the autophagy-lysosome pathway.
AUTOTAC mediates the targeted degradation of not only monomeric proteins, but also
proteins with aggregation prone proteins. Using mouse models expressing human

pathological tau mutants, researchers have demonstrated that AUTOTAC is effective in
removing misfolded tau. In contrast, proteasome-based techniques, such as PROTAC
and molecular glue, are generally ineffective in dealing with misfolded proteins. In addition
to Tau, AUTOTAC is also effective in removing a variety of oncoproteins, such as
degrading the androgen receptor (AR).
The representative company developing AUTOTAC technology is AUTOTACBio,
headquartered in Seoul, Korea. The company's CEO, Dr. Yong Tae Kwon, is the
co-corresponding author of the above paper. Currently, the company has laid out a variety
of disease areas such as neurodegenerative diseases (e.g. AD), cancer, metabolic
syndrome, and muscular dystrophy, and has built a rich pipeline.
CMA-based degrader
In chaperone-mediated autophagy (CMA), heat shock protein 70 (HSC70) recognizes
soluble protein substrates with KFERQ sequences. Subsequently, the HSC70-substrate
complex binds to lysosome-associated membrane protein 2A (LAMP2) on the lysosomal
membrane and the substrate translocates to the lumen of the lysosome for degradation.
Figure 17. CMA-based degrader, source: reference [1]

CMA-based degrader consists of three functional domains: a cell membrane penetrating
sequence, a POI binding sequence, and a CMA targeting motif. Upon use of CMA-based
degrader, such degrader first enters the cell, then binds the target protein via the POI
binding sequence, and finally is transported to the lysosome for degradation. This
technique has been shown to reduce the levels of scaffold proteins PSD-95, DAPK1, and
α-synuclein. However, to be an effective therapeutic strategy, CMA-based degradants
need to overcome at least two major hurdles, firstly, the stability of the degradant; and
secondly, effective delivery.
Conclusion
Targeted protein degradation (TPD) has arguably been one of the most dynamic areas of
research in both science and industry over the past few years, with a proliferation of new
technologies opening new doors for drug development.
In terms of technology types, PROTAC and molecular glues are the most advanced TPD
technologies (both have several projects in clinical development), both are based on the
ubiquitin-proteasome system and are mainly used to degrade intracellular proteins.
However, the development of these two types of technologies still faces many challenges,
such as PROTAC, which often faces challenges in cell permeability and oral bioavailability
due to its large molecule, and molecular glue, which is small but currently difficult to
design effectively.
TPD technologies using lysosomal degradation pathways have also been rapidly
developed in the past few years, including LYTAC, Bispecific Aptamer Chimeras, AbTAC
and GlueTAC technologies that degrade extracellular and membrane proteins using the
endosomal-lysosomal pathway, and autophagy-lysosomal pathways to degrade misfolded
proteins, protein aggregates or damaged organelles with technologies such as AUTAC,
ATTEC, and AUTOTAC. The development of TPD technologies based on the lysosomal
degradation pathway is still in its infancy compared to PROTAC and molecular glues.

There is still much to learn about the specific mechanisms of each technology. As an
important intracellular organelle, lysosomes regulate many important cellular and
physiological functions, such as metabolism and homeostasis, in addition to protein
degradation. It is unclear whether "hijacking" the lysosomal degradation pathway affects
the whole organism, therefore, further characterization of TPD technologies based on the
lysosomal degradation pathway is necessary.
Currently, several TPD molecules are in cancer clinical trials. In addition to cancer, many
TPD molecules show great potential in areas such as neurodegenerative diseases,
inflammatory diseases or viral infections. Although there are many challenges to
overcome, there is no doubt that TPD technology will hold great promise for future drug
development.
References:
[1] Zhao, L., Zhao, J., Zhong, K. et al. Targeted protein degradation: mechanisms, strategies and
application. Sig Transduct Target Ther 7, 113 (2022). https://doi.org/10.1038/s41392-022-00966-4
[2] He, M., Cao, C., Ni, Z. et al. PROTACs: great opportunities for academia and industry (an update from
2020 to 2021). Sig Transduct Target Ther 7, 181 (2022). https://doi.org/10.1038/s41392-022-00999-9
[3] Whitworth C, Ciulli A. New class of molecule targets proteins outside cells for degradation. Nature.
2020;584(7820):193-194. doi:10.1038/d41586-020-02211-w
[4] Caianiello, D.F., Zhang, M., Ray, J.D. et al. Bifunctional small molecules that mediate the
degradation of extracellular proteins. Nat Chem Biol 17, 947–953 (2021).
https://doi.org/10.1038/s41589-021-00851-1
[5] Miao Y, Gao Q, Mao M, et al. Bispecific Aptamer Chimeras Enable Targeted Protein Degradation on
Cell Membranes. Angew Chem Int Ed Engl. 2021;60(20):11267-11271. doi:10.1002/anie.202102170
[6] Daiki Takahashi, Jun Moriyama, Tomoe Nakamura, Erika Miki, Eriko Takahashi, Ayami Sato, Takaaki
Akaike, Kaori Itto-Nakama, Hirokazu Arimoto, AUTACs: Cargo-Specific Degraders Using Selective
Autophagy, Molecular Cell, Volume 76, Issue 5, 2019, Pages 797-810.e10, ISSN 1097-2765,
https://doi.org/10.1016/j.molcel.2019.09.009.

Related Articles:
PROTACs and Targeted Protein Degradation
PROTACs VS. Traditional Small Molecule Inhibitors
Four Major Trends In The Development of PROTAC
Molecular Glues: A New Dawn of Small Molecule Drugs After PROTAC

12 Types of Targeted Protein Degradation Technologies.pdf

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Similar to 12 Types of Targeted Protein Degradation Technologies.pdf

Similar to 12 Types of Targeted Protein Degradation Technologies.pdf (20)

More from DoriaFang

More from DoriaFang (20)

Recently uploaded

Recently uploaded (20)

12 Types of Targeted Protein Degradation Technologies.pdf