Proteolysis-targeting chimeras (PROTACs) are bifunctional protein degraders that use the E3 ubiquitin ligase pathway for the degradation of the protein of interest. A PROTAC molecule consists of three components: a ligand moiety that targets the protein of interest (POI), another ligand that binds to E3 ligase, and a linker, which bridges between these two ligands [1]. The main function of these ligands is to attract E3 ligase and POI and initiate polyubiquitination for degrading POI via the ubiquitin–proteasome system (UPS) (Figure 1) [2]. The ubiquitin–proteasome system is an essential pathway of every eukaryotic cell for maintaining homeostasis and regulating gene transcription and translation, cell cycle, and apoptosis [3]. In the ubiquitin proteolysis pathway, the ubiquitin molecule binds to the ubiquitin-activating enzyme E1. The E1-bound ubiquitin transfers the ubiquitin to the E2-conjugating enzyme, which is later transferred to E3 ligase, and, finally, ubiquitin binds to POI. These are ATP-driven cascades of reaction where the ubiquitin molecule is transferred from one molecule to another and, finally, to POI. Similarly, several ubiquitin molecules bind to the POI, which signals the proteasome to initiate the degradation of the polyubiquitinated POI. This innate protein degradation pathway is utilized for degrading POI.

The targeted degradation of the proteins has been explored using various techniques like ligand-induced degradation [4] (LID), hydrophobic tagging (HyT) [5], etc. These techniques later lead to the development of PROTACs [6]. PROTACs are more efficient than conventional small molecule inhibitors [7]. For instance, traditional small molecule inhibitors could only inhibit the activity of certain enzymes or could block the partial function of the protein, while PROTACs can completely eliminate the disease-related proteins [8]. A significantly lower concentration of the drug is required in case of targeted protein degradation using PROTACs as compared to small molecule inhibitors. Many proteins which remain undruggable over the decades, like scaffold proteins, transcriptional factors, or proteins without active binding sites, could be easily targeted by PROTACs and other similar targeted technologies [9]. Such molecules have the great advantages of high selectivity, catalytic, and drugging the undruggable targets.

The first PROTAC molecule was successfully developed in 2001, and, to date, more than 3270 PROTACs have been developed [10]. Some of the PROTAC molecules are currently in different phases of clinical trials, and their initial results have provided a great modality for PROTAC-based degraders (Table 1) [11]. Thus, PROTACs have grabbed the attention of various pharmaceutical companies. Companies such as Arvinas [12], Pfizer [13], Accutar Biotech [14], Bristol Myers Squibb [15], Dialectic Therapeutics [16], Foghorn Therapeutics [17], Kymera Therapeutics [18], Nurix Therapeutics [19], C4 Therapeutics [20], and Cullgen [21] have already entered in the race of clinical trials for their respective PROTAC molecules. It has been predicted that within a few years, approximately 15 PROTAC molecules will be in clinics [22]. Due to the inarguable potential of PROTACs in the current era, researchers are exploring the possibilities of developing new protein degraders for various diseases, such as immunological disorders [23], inflammatory disorders ^[24][25][26][24,25,26], cancer ^[27][28][27,28], auto-immune diseases [29], neurological diseases [30], bacterial infections [31], and viral infections [32]. It is undeniable to state that PROTAC-based degraders are highly investigated in the field of cancer research, and many protein degraders are in the pipeline for clinical trials. However, the exploration of PROTACs in the field of anti-microbial remains marginal. This rentryview is an attempt to highlight the state-of-the-art protein-based degraders targeting microorganisms. It also emphasizes PROTACs as an alternative to antibiotics.

In the current scenario, due to the inappropriate/overuse of antibiotics, the use of antibiotics in the agricultural field and feeding livestock has led to the emergence of resistant strains of pathogens, which is a major threat to humankind. Consequently, pharmaceutical industries consider the development of new antibiotic as potentially effective for a shorter duration and also requires hefty investment [46]. Thus, there is a need to develop new strategies for targeting multidrug-resistant pathogens. Thus, PROTAC could be a glimmer of hope for destroying resistant pathogens [31]. Due to the characteristic nature of direct degrading of the disease-related protein or POI instead of inhibiting them could provide enhanced sensitivity towards multidrug resistant pathogens [47]. Since PROTACs utilize a chemical knockdown approach, an innate cellular mechanism, there are likely fewer chances of the generation of spontaneous mutations in the target protein [8]. There are several approaches for degrading the POI, and they are classified based on the type of degradation system used, namely, the eukaryotic system and prokaryotic system.

2. Eukaryotic System

2.1. Anti-Viral PROTACs

2.1.1. Degradation of Viral Protein

In this section, PROTACs that target viral proteins have been enlisted. PROTAC-based protein degraders are highly explored in this section as compared to other strategies of protein degradation. Many viral proteins have been targeted for protein degradation (Table 2). For instance, Montrose et al. developed a peptide-based PROTAC molecule that targets X-protein, which is an essential protein required for the replication of the hepatitis B virus (HBV). It was also found that the presence of X-protein could also induce hepatocellular Carcinoma (HCC). This PROTAC molecule consists of an ODD degrons (oxygen-dependent degradation) domain, an oligomerization domain, and a cell-penetrating peptide. The ODD degrons domain binds to Von Hippel–Lindau (VHL) E3 ligase, the oligomerization domain interacts with the X-protein, and octa-arginine is used as a CPP for to ease cellular entry. In vitro studies verified the ability of peptide-based PROTACs to efficiently degrade X-protein [48]. In another study, instead of the peptide as a ligand for POI, the authors used telaprevir, an anti-viral peptidomimetic protease inhibitor. They developed three different molecules (DGY-03-081 (2), DGY-04-035 (3), and DGY-08-097 (4)) that target the NS3/4A protease of the hepatitis C virus (Figure 2). Lenalidomide, pomalidomide and novel tricyclic imide moiety were used as the ligands for CRBN E3 ligase. The function of NS3/4A serine protease is to cleave viral polyprotein, which acts as an essential step in viral replication [49]. Thus, degradation of NS3/4A protease via PROTAC will inhibit virion formation and multiplication. These compounds were evaluated in Hep C virus-infected HEK293T cells. Interestingly, all three degraders exhibited anti-viral activity and did not show cytotoxicity to the uninfected cells. Compound DGY-08-097 (4) had the highest degradation ability and the least DC₅₀ value (50 nM at 4 h). One of the reasons for the increased affinity might be due to the tricyclic imide moiety in the DGY-08-097 (4) that showed increased affinity towards CRBN E3 ligase [50].