Introduction - Protein degradation is a vital cellular process that functions as a core maintenance mechanism in the body. It ensures the elimination of unwanted, damaged, or misfolded proteins, thereby preserving cellular health and equilibrium. This carefully regulated system prevents the build-up of dysfunctional proteins, which could otherwise interfere with normal cellular operations and contribute to the onset of various diseases. This process of protein degradation is orchestrated through various pathways, with the ubiquitin-proteasome system (UPS) being a primary mechanism.
Scientists have leveraged this natural cellular machinery to develop innovative molecules that selectively target and degrade proteins implicated in life-threatening diseases. These ground-breaking molecules are known as PROTACs (Proteolysis-Targeting Chimeras). PROTACs are heterobifunctional molecules that hijack the UPS and are used to target specific disease-causing proteins in cells.
Mechanism of Action -
Structurally, a PROTAC consists of three components: (i) a ligand for binding of the protein of interest (POI), (ii) a ligand for binding the E3 ligase, and (iii) a linker connecting the two ligands.
Once inside the cell, the PROTAC molecule recruits the E3 ligase and the protein of interest. The PROTAC initially forms a binary interaction with one of these proteins. Once this binary complex is established, it seeks out the second protein, which binds to the opposite end of the PROTAC, resulting in the formation of a ternary complex. This ternary complex brings the protein of interest and the E3 ligase into close proximity, facilitating the creation of novel protein-protein interactions that would not occur without the PROTAC. As a result, the E3 ligase can transfer ubiquitin molecules to the target protein. Multiple ubiquitin molecules are added, both at different sites and sequentially, to build polyubiquitin chains. Proteins tagged with ubiquitin molecules are recognized by proteasome, thus leading to their degradation.
PROTACs targeting viral host-protein -
The recent approach to develop new antiviral drugs is to target the host proteins. This approach addresses the challenge of drug resistance, which often arises from mutations in viral genomes. Since viruses depend on the host's cellular machinery to replicate their genetic material, targeting host proteins offers a more stable and effective strategy. It eliminates the need for constant modifications to antivirals, which are otherwise required to counteract the frequent mutations in viral genomes. An example of this strategy is the repurposing of Indomethacin (INM) for the treatment of COVID-19 (SARS-CoV-2).
INM, a non-steroidal anti-inflammatory drug, is known to act by inhibiting prostaglandin E synthase type-2 (PGES-2), a key enzyme for eicosanoid biosynthesis. In the context of SARS-CoV-2, studies demonstrated that INM inhibits the virus's replication cycle by activating the protein kinase R (PKR) pathway, which suppresses protein synthesis in virus-infected cells. Additionally, INM's inhibition of the host enzyme PGES-2 disrupts its interaction with non-structural protein 7 (NSP7), a critical component of the viral primase complex, which also includes NSP8.
The non-structural protein 7 (NSP7)-NSP8 complex is a crucial component of the viral RNA polymerase machinery, conserved across various coronavirus (CoV) variants. This highlights its importance as a target for antiviral strategies. To exploit this, INM-based PROTACs were developed by conjugating indomethacin (INM) with the von Hippel-Lindau (VHL) E3 ligase ligand using aliphatic or polyethylene glycol linkers. By targeting PGES-2, these PROTACs disrupt its enzymatic and scaffolding functions, thereby halting the cascade of reactions necessary for viral replication.
The IC50 value represents the compound concentration that inhibits 50% of viral replication. The CC50 value represents the compound concentration that inhibits 50% of cell viability.
Conclusion-
PROTACs have emerged as front runners in developing targeted protein degradation (TDP) therapies. They represent a revolutionary leap forward in the field of drug discovery and precision medicine. By degrading rather than inhibiting proteins, PROTACs offer a robust strategy to overcome drug resistance. There exist challenges in stability, selectivity, and synthesis but the rapid progress in research and development paves the way for transformative treatments. As this technology continues to evolve, it holds the promise of shaping a future where medicine is more precise, effective, and innovative than ever before.
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-By Aaditya Bhat
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