PROTACs in targeted protein degradation: Advances in development and AI-enhanced drug discovery

Targeted protein degradation (TPD) eliminates disease-relevant proteins by engaging endogenous proteolytic machinery, most prominently the ubiquitin-proteasome system (UPS). Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules composed of a protein of interest (POI) ligand, an E3 ligase recruiter, and a linker. By bringing the POI and E3 ligase into proximity, PROTACs promote POI ubiquitination and subsequent proteasomal degradation, and multiple candidates have progressed into clinical trials. This review summarizes the structural and mechanistic principles that govern PROTAC efficacy, selectivity, and degradation kinetics, and highlights key modality innovations and representative clinical progress with an emphasis on chemical structures, quantitative degradation metrics, and structure-activity relationships. We then examine key translational bottlenecks, including ternary-complex (TC) dependence, the hook effect, limited E3 ligase options, context-dependent selectivity, permeability, and beyond-Rule-of-Five (bRo5) properties, and discuss practical medicinal chemistry strategies to address these challenges. Finally, we describe how computational modeling and AI can be integrated across the design-make-test cycle, and summarize emerging data resources that enable more prospective, data-driven PROTAC discovery. AI-driven modular design framework for PROTAC development, integrating AI-based Data Processing, Ligand Discovery (POI ligands/warheads and E3 recruiters), POI Prioritization, Ternary Complex Modeling & Scoring, and AI-Driven Linker Optimization to generate PROTAC Assembly Blocks and assemble In Silico PROTAC Designs for downstream prioritization and experimental validation. • 1Summarizes mechanistic and structural principles underlying PROTAC-induced degradation. • 2Distills medicinal-chemistry strategies that tune ternary-complex cooperativity and degradation selectivity. • 3Provides a structured view of key translational limitations (hook effect, permeability, drug-likeness, E3 context, and bRo5). • 4Reviews computational and AI tools that mitigate major bottlenecks across the PROTAC workflow. • 5Discusses data resources and future directions for scalable, data-driven PROTAC discovery.

Background:

Malaria is a potentially life-threatening disease that occurs in tropical and subtropical regions of the world. Despite continued efforts to reduce or even eliminate the burden of malaria in endemic areas, this disease still represents a major public health concern. Efforts to eradicate malaria were impacted by the COVID-19 pandemic, resulting in an estimated additional 13.4 million cases during this period. In fact, in 2022, 249 million new cases were estimated in 85 endemic countries and areas, representing an increase of 5 million cases compared to 2021. Globally, in 2022, 608,000 deaths due to malaria were estimated. Most of these cases and deaths were concentrated in Africa, and the most vulnerable group was children aged under 5 years, who accounted for approximately 76 % of all malaria deaths.

Malaria is caused by protozoan parasites belonging to the Plasmodium genus. To date, approximately 200 Plasmodium species have been identified that can cause malaria in different vertebrate hosts, but 6 species routinely cause disease in humans: P. malariae, P. falciparum, P. vivax, P. knowlesi, P. ovale curtisi, and P. ovale wallikeri. Among them, P. falciparum and P. vivax represent the predominant causative agents of malaria worldwide, with P. falciparum causing over 90 % of cases of malaria and of severe malaria.

Plasmodium presents a complex life cycle that alternates between a sexual phase (sporogony) in the mosquito vector and an asexual phase (schizogony) that occurs in the vertebrate host. Human malaria is initiated with the bite of an infected female Anopheles mosquito which delivers sporozoites into the bloodstream. The sporozoites then migrate to the liver, where they invade and infect hepatocytes. Following a period of intrahepatic multiplication and differentiation, newly formed merozoites are released into the bloodstream, where they repeatedly infect red blood cells (RBCs).

Methods:

We report the optimization of the indolizinoindolone scaffold to increase activity against erythrocytic stages of Plasmodium (P.) falciparum and against hepatic stages of the rodent parasite P. berghei. Twenty-six enantiopure indolizinoindolones were synthesized, with IC50 values in the low micromolar and sub-micromolar range against both stages, and no significant cytotoxicity against mammalian cell lines. The most active compound showed nanomolar activity against P. falciparum blood stages in vitro, low micromolar activity against hepatic P. berghei infection in vitro, and a 7-fold higher selectivity index than that of chloroquine. This compound was also tested in P. berghei-infected mice, inhibiting the development of parasitemia relative to untreated mice.

Results:

Key findings include the identification of indolizinoindolones with IC50 values in the low micromolar and sub-micromolar range against both erythrocytic and hepatic stages. The most active compound demonstrated nanomolar activity against P. falciparum blood stages in vitro and low micromolar activity against hepatic P. berghei infection in vitro. It also exhibited a 7-fold higher selectivity index than chloroquine and inhibited the development of parasitemia in P. berghei-infected mice relative to untreated controls.

Data Summary:

Twenty-six enantiopure indolizinoindolones were synthesized. IC50 values were in the low micromolar and sub-micromolar range against both stages. The most active compound showed nanomolar activity against P. falciparum blood stages and low micromolar activity against hepatic P. berghei infection. Its selectivity index was 7-fold higher than that of chloroquine.

Conclusions:

Overall, we identified a new set of lead antimalarial compounds. Further optimization of the pharmacokinetic properties of this scaffold is warranted.

Practical Significance:

The new indolizinoindolone compounds identified in this study represent promising leads for the development of dual-stage antimalarials, addressing the urgent need for new treatments due to the emergence of resistance to most available drugs. Their dual activity against both blood and liver stages, combined with a favorable selectivity index, suggests potential for further optimization and eventual clinical use in malaria-endemic regions.