In recent years, drug discovery research utilizing targeted protein degradation (TPD), which enables the selective elimination of specific intracellular and extracellular proteins, has attracted considerable attention. Compounds that induce TPD leverage multiple degradation mechanisms within the endogenous cellular proteasome and lysosome pathway. Among these, the clinical application of chimeric degraders represented by PROTAC^Ⓡ (Proteolysis Targeting Chimera) has advanced rapidly in recent years, approaching the stage of social implementation. However, during the clinical development process, several common challenges related to physicochemical properties and pharmacokinetics for practical application have also emerged. This article provides an overview of TPD technologies followed by the current status of clinical trials for chimeric degraders and discusses the issues that have emerged so far and future prospects for overcoming them.

Targeted protein degradation has recently emerged as a new therapeutic modality that exploits the ubiquitin–proteasome system. Major classes of degrader molecules, such as PROTACs and molecular glues, function by bringing a target protein (neo-substrate) into close proximity with an E3 ubiquitin ligase, thereby enforcing ubiquitination of the target and inducing its proteasome-dependent degradation. Consequently, a detailed understanding of degradation mechanisms based on the fundamental principles of the ubiquitin–proteasome system is essential for improving the efficiency and precision of targeted protein degradation. In recent years, the importance of higher-order architectures of ubiquitin chains, referred to as the ubiquitin code, in promoting protein degradation has become increasingly evident. In this article, we first outline the basic principles of the ubiquitin–proteasome system and the concept of the ubiquitin code, and then discuss intracellular regulatory factors that control targeted protein degradation and the mechanisms by which these factors promote degradation, including insights from our own work.

Targeted protein degraders (TPDs) have emerged as a novel drug discovery modality that induces protein degradation by promoting drug-dependent interactions between target proteins and E3 ubiquitin ligases. The specificity of TPDs is determined by drug-induced protein-protein interactions (PPIs). In this review, we provide an overview of biochemical PPI analyses based on a wheat germ cell-free protein synthesis system combined with the AlphaScreen assay, as well as cellular and in vivo TPD-dependent interactome analyses using the proximity-dependent biotinylation enzyme AirID. Through representative examples, we highlight the importance of evaluating drug-dependent PPIs for understanding TPD specificity and discuss the significance of these approaches in TPD-based drug discovery.

Hematopoietic prostaglandin D synthase (HPGDS) is a key enzyme responsible for the biosynthesis of PGD₂ and has been implicated in the pathogenesis of severe asthma, atopic dermatitis, and Duchenne muscular dystrophy (DMD). Although small-molecule HPGDS inhibitors have been developed, their clinical efficacy has been limited in certain disease settings, potentially due to insufficient and non-sustained suppression of PGD₂ production. To overcome these limitations, we developed a proteolysis-targeting chimera (PROTAC) designed to induce selective degradation of HPGDS via the ubiquitin–proteasome system. Using high-resolution X-ray crystal structural information of HPGDS, we rationally designed a highly specific HPGDS-binding ligand and conjugated it to a E3 ligase, Cereblon (CRBN)-recruiting ligand through an optimized linker. Structure-guided modeling and in silico ternary complex simulations enabled refinement of the spatial orientation between HPGDS and CRBN, resulting in PROTAC-HPGDS compounds exhibiting remarkably potent degradation activity in the picomolar range. These degraders achieved efficient and sustained suppression of HPGDS protein levels, suggesting a potential advantage over conventional enzymatic inhibition. In addition, we established a rapid and time-resolved evaluation platform for HPGDS degradation by constructing a fluorescent protein–fused HPGDS expression system. This approach allows real-time monitoring of degradation kinetics without reliance on conventional Western blot analysis, thereby significantly improving throughput and quantitative assessment of PROTAC activity. The fluorescence-based system was validated both in cultured cells and in preliminary in vivo imaging experiments. Collectively, this study demonstrates an integrated drug discovery strategy that combines structural biology, rational ligand design, and targeted protein degradation technology. The development of PROTAC-HPGDS and its associated screening platform provides a promising therapeutic approach for diseases driven by excessive PGD₂ production and supports the clinical potential of degradation-based modalities for inflammatory and neuromuscular disorders.

Lysine-modifying enzymes―such as histone acetyltransferases (HATs), histone deacetylases (HDACs), lysine methyltransferases (KMTs), and lysine demethylases (KDMs)―regulate a wide range of cellular processes and are implicated in various diseases. As such, they have long been considered attractive therapeutic targets. Traditionally, drug discovery efforts have focused on developing inhibitors that block the enzymatic activity of these proteins. However, growing evidence suggests that inhibiting catalytic activity alone is often insufficient to achieve meaningful or lasting biological outcomes in cellular or disease models. Recent studies have shown that many lysine-modifying enzymes also act as scaffolding proteins, forming multiprotein complexes with transcription factors and chromatin-associated proteins. Through these non-catalytic interactions, they influence gene expression, chromatin organization, and cellular phenotypes. These findings underscore the limitations of conventional enzyme inhibition strategies and highlight the need for new therapeutic approaches that can suppress both the catalytic and non-catalytic functions of these proteins. Proteolysis-targeting chimeras (PROTACs) have emerged as a promising solution to this challenge. PROTACs are bifunctional molecules that promote the selective degradation of target proteins via the ubiquitin–proteasome system. Unlike traditional inhibitors, PROTACs eliminate the entire target protein, thereby disrupting all associated functions, both enzymatic and scaffolding. This mode of action can produce distinct biological effects and may offer therapeutic benefits that cannot be achieved through inhibition alone. In this article, we highlight PROTAC-based strategies targeting key lysine-modifying enzymes, including HDAC8, G9a/GLP, and KDM5C. By summarizing our recent work on the design and biological evaluation of these degraders, we demonstrate how targeted protein degradation can deepen our understanding of protein function and open new avenues for therapeutic development beyond conventional inhibition.

Drug discovery technologies leveraging machine learning (ML) and generative artificial intelligence (AI) have advanced rapidly in recent years. In the field of targeted protein degraders, such as proteolysis-targeting chimeras (PROTACs), ML- and AI-driven approaches have also attracted increasing attention. To facilitate the optimization of physicochemical and pharmacokinetic properties, including the degradation activity against proteins of interest (POIs) and cell membrane permeability, several ML-based prediction methods have been developed. Moreover, the optimization of linker structures, which are components of PROTACs, is critical for controlling these properties in PROTAC development. However, conventional linker optimization often relies on trial and error based on the intuition and experience of medicinal chemists, resulting in substantial time and labor requirements. To address this, PROTAC linker design methods using various molecular generative AI techniques have been developed. In this article, we review ML- and generative AI-based approaches for PROTAC development, with a particular focus on linker design. In addition, we introduce the ChemTS series, a group of molecular generative AI developed by our research group, and PROTAC-TS, a generative AI-based PROTAC linker design method based on reinforcement learning. We demonstrate the performance of PROTAC-TS by designing PROTAC linkers for three POI ligand–E3 ligand pairs and report the corresponding results. We anticipate that continued accumulation of experimental data, together with further advances in ML technologies, will enable more rational and efficient data-driven strategies for PROTAC design.

In this article, we describe targeted protein degradation technology specifically designed for mitochondria-localized proteins, with a primary focus on our own development. Our approach employs a bifunctional molecule comprised of a ligand for the target protein linked to an activator of caseinolytic protease P (ClpP), a mitochondria-localized protease complex. The degrader induces the selective degradation of target proteins by bringing target proteins and activated ClpP into proximity within the mitochondria. Furthermore, we discuss the advantages of this technology─specifically the direct recruitment of proteases─in comparison with other reported methods and outline future directions and prospects for this technology.

Topical antibiotic therapy is an effective treatment option for bacterial otitis media and otitis externa because it enables the direct delivery of high drug concentrations to the site of infection. This approach can be regarded as an efficient drug delivery system that maximizes local antimicrobial exposure while minimizing systemic adverse effects. Traditionally, fluoroquinolone ear drops (such as ofloxacin) have been widely used for these indications. However, the recent increasing prevalence of antimicrobial resistance and need to improve clinical efficacy have highlighted the limitations of conventional formulations. Based on pharmacokinetic/pharmacodynamic (PK/PD) principles, a high-concentration levofloxacin formulation, Comlex^Ⓡ Otic solution 1.5%, was developed to address these challenges. Levofloxacin, the optically active S-enantiomer of ofloxacin, exhibits superior antibacterial activity, and its high local concentration is designed to achieve optimal PK/PD targets at the infection site. This strategy is expected to enhance the bactericidal activity and reduce the likelihood of resistance development by ensuring sufficient drug exposure above the minimum inhibitory concentration. Comlex^Ⓡ Otic solution 1.5% has been formulated with careful consideration of safety. Notably, it does not contain preservatives, reducing the risk of local irritation and has a low potential for ototoxicity, making it suitable for use even in cases where the integrity of the tympanic membrane may be compromised. These characteristics contribute to its favorable safety profile and support its use in routine clinical practice. In context of the global increase in antimicrobial-resistant pathogens, appropriate use of potent topical antibiotics for the initial treatment of ear infections is increasingly important. When used as first-line therapy, Comlex^Ⓡ Otic solution 1.5% has the potential to improve the reliability of treatment outcomes, promote rapid resolution of infection, and contribute to the suppression of antimicrobial resistance. Consequently, this high-concentration levofloxacin formulation represents a promising therapeutic option for the effective management of bacterial otitis media and otitis externa.