PROTAC Synthesis and Screening

We offer expertise in all niche modalities related to PROTACs and molecular glues for targeted protein degradation, including stand-alone Chemistry, Biology (in vitro, in vivo pharmacology and toxicology) and DMPK services to fully integrated drug discovery programs

PROteolysis – TArgeting Chimeras (PROTACs) are a series of hetero-bifunctional molecules that hijack the body’s own natural disposal system to initiate selective degradation of the protein of interest (POI). PROTACs have the potential to overcome most of the limitations of small molecule inhibitors, while offering several advantages of the traditional concepts of drug discovery. Aurigene offers expertise in all niche modalities related to PROTACs and molecular glues for targeted protein degradation, including stand-alone Chemistry, Biology (in vitro, in vivo pharmacology and toxicology) and DMPK services to fully integrated drug discovery programs.

We have extensive experience in not only the synthesis and purification of PROTACs but also the capability of extensively profiling our synthesized PROTACs including various biological assays, in addition to a full-spectrum ADME and PK services tailored to PROTAC molecules. We are uniquely poised in the Indian CRO market not only as a key player with extensive knowledge in small molecule-based Drug Discovery research but also can offer our significant experience on the PROTAC-related domain to any potential collaborators.

We are well versed in the synthesis and functionalization of various E3-ligase ligands such as CRBN, VHL, MDM2, AhR, and cIAP1 (in multi-gram scale) and in the synthesis of commercially available ligands, as well as in developing novel structural analogues as per custom requests like open CRBNs. We also have significant experience in the related fields of Targeted Protein Degradation (TPD) such as molecular glues, ATTECs, AUTECs, HyTs and in niche modalities like Oligo-PROTACs, Peptide-PROTACs, etc. We also offer a partial PROTAC library of ~500 entries as a quick plug-and-play for PROTAC development from a POI-ligand of choice.

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PROTAC Synthesis & Screening for Targeted Protein Degradation

PROTACs – Advantages over Conventional Inhibitors

PROTACs have the potential to overcome most of the limitations of small molecule inhibitors, and they offer several advantages of the traditional concepts of drug discovery, including increased selectivity and reduced toxicity among others. This approach also has the potential to target the “undruggable” proteome that limits traditional drugs.

PROTAC Synthesis and Screening Services for Targeted Protein Degradation

Synthesis of common E3-Ligase ligands (CRBN, VHL, cIAP, and MDM-2) and their structural analogues from milligram to gram scale and beyond
Capability to develop novel flexible or rigid linkers for novel discovery needs
Experience in the synthesis of molecular glues and monovalent protein degraders
In-house library of >500 partial PROTACs and linkers for rapid target engagement
Flexible business models including stand-alone Chemistry services, as well as fully integrated discovery services and various mix-and-match programs
Stand-alone biology support including in vitro and in vivo profiling, DMPK, or toxicology

Purification of PROTACs

Synthetic team with >10 years of experience with PROTAC chemistry to minimize hurdles
Very experienced analytical team, specifically in purifying PROTACs and Molecular Glues
Dedicated preparative HPLC systems for supporting PROTAC-related projects
Buchi Lyovapor L-300s for supporting the PROTAC platform in minimizing stability issues
SFC and HRMS support provided wherever needed

Integrated Drug Discovery Expertise for PROTAC Screening

In addition to the Medicinal chemistry of PROTACs, Aurigene services also offer substantial experience in the biology of protein degraders, gained through the extensive in-house research drug discovery research. We offer comprehensive in-vitro biology support to interested collaborators, including various biological assays, DMPK and toxicology.

Binary binding and functional assays to measure interaction of E3 ligase to PROTACs and PROTAC/ its ligand to target protein using various assays like TR-FRET, HTRF, AlphaLISA, and various other functional assays depending on the target protein and E3 ligase
Target binding studies and ternary complex formation (using various assay platforms like Hi-BiT, Nano-BRET, SPR etc.) to understand the ratio of ternary to binary binding efficiencies
Functional cell-based assays for evaluating target degradation (Western Blotting, Automated Westerns, HiBiT screening) and downstream target engagement assays
Preliminary ADME studies (e.g. permeability, solubility, microsomal stability)
PK studies in rodents (terminal) and in dogs (non-terminal studies)
Fully integrated and semi-integrated drug discovery programs as well as stand-alone biology services.
In addition to prosecuting PROTACs and screening, we also offer support at multiple levels to understand biology of target protein that includes protein half-life, extent and duration of degradation, functional isoform compensation (if any), cellular E3 expression, differential advantage of inhibiting the target vs degrading the target at molecular level and MoA studies.

Molecular Glues

Molecular glues are monovalent small molecules (single entities) that reshape the surface of an E3 ligase receptor, assisting novel protein-protein interactions (PPIs) by squeezing between protein–protein interfaces (Schreiber, 2021).
They are much smaller in nature and thus more easily abide by Lipinski’s rule of five, increasing the probability of good oral bioavailability.
Expected to have better permeability and membrane uptake, more suited for CNS-targets.

	Type	Linker	Mol. Wt.	Lipinski Rule	Binding Pocket	Affinity
PROTACs	Bivalent	Needed	>700-1000	No	Needed	Strong
Molecular Glues	Monovalent	Not Needed	<500	Yes	Not Required	Week

At Aurigene, we have extensive experience in the synthesis and profiling of molecular glues, which provides us a unique advantage in offering stand-alone, semi-integrated and fully integrated discovery programs for our collaborators.

References

1. 1.Schreiber, S. L. (2021). The rise of molecular glues. Cell, 184(1), 3-9.

Why Aurigene Pharmaceutical Services?

Ready-to-use partial PROTAC library

Flexible business models including mix and match programs

Comprehensive biology support

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Frequently asked questions

What is Target Protein Degradation?

Target Protein degradation is a process in which the protein of interest is degraded using E3 ubiquitin ligase and a chemical linker by polyubiquitination followed by proteasome degradation.

What are the advantages of the Protein degradation approach against conventional approaches?

High target selectivity demonstrates high potencies, less toxic ,and minimizing the risk of developing resistance.

Does PROTAC forms a ternary Complex?

A targeting ligand (warhead) for the protein of interest and a ligand that recruits an E3 ubiquitin ligase connected via a carefully-chosen chemical linker (PROTAC). The resulting compound can induce formation of a ternary complex (the target, degradation compound and E3 ligase). The design of degrader compounds is critical to form an effective ternary complex.

What is Targeted Protein Ubiquitination?

The addition of ubiquitin to a substrate protein is called ubiquitination. Ubiquitination of target proteins involves a three-step enzymatic process, i.e., Activation, conjugation, and Ligation. Finally, polyubiquitinated proteins are recognized by the proteasome then degrades into small peptides by proteolysis.

What Is the PROTAC's Cellular Permeability and Target Affinity?

Cellular Permeability and Target Affinity are the important factors to decide the effective binding of PROTAC with target protein and ubiquitination. These parameters play a crucial role in the designing of PROTAC molecules.

What is the potential of PROTAC for pharmaceutical research?

PROTACs regulate protein function by degrading target proteins instead of inhibiting them, providing more sensitivity to drug-resistant targets and a greater chance of affecting nonenzymatic functions. PROTACs have been proven to show better selectivity compared to classic inhibitors. It has attracted great attention both from academia and industry.

How are PROTACs gaining traction as a cancer drug discovery technique in the modern era?

Catalytic in nature, targeted degradation and selectivity provide a niche for PROTAC applications in cancer diseases and immune disorders, viral infections, and neurodegenerative diseases.

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PROTAC Synthesis and Screening

PROTACs – Advantages over Conventional Inhibitors

PROTAC Synthesis and Screening Services for Targeted Protein Degradation

Purification of PROTACs

Integrated Drug Discovery Expertise for PROTAC Screening

Molecular Glues

Why Aurigene Pharmaceutical Services?

Other Services

Virtual Tour

Connect with our scientific experts for your drug discovery, development, and manufacturing needs

section

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Resources

The Journey from Scientific to patient impact

End-to-End Rebuild of a Complex Bicyclic Peptide Synthesis

Identification of Degradants of Thermal and Oxidation Stress Studies of Empagliflozin and Linagliptin Tablets by HPLC-PDA and LC-MS Instrumental Techniques

Frequently asked questions

What is Target Protein Degradation?

What are the advantages of the Protein degradation approach against conventional approaches?

Does PROTAC forms a ternary Complex?

What is Targeted Protein Ubiquitination?

What Is the PROTAC's Cellular Permeability and Target Affinity?

What is the potential of PROTAC for pharmaceutical research?

How are PROTACs gaining traction as a cancer drug discovery technique in the modern era?

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