Targeted protein degradation (TPD) is an emerging approach that selectively eliminates specific proteins using synthetic molecules, such as proteolysis-targeting chimeras (PROTACs). It has attracted increasing attention in medicinal chemistry and chemical biology, with several PROTACs being tested in clinical settings. Unlike traditional small molecules, such as enzyme inhibitors and receptor antagonists, PROTACs exhibit a fundamentally different mechanism. Conventional drugs block enzymatic activities or receptor interactions, whereas PROTACs induce the degradation of target proteins, decreasing their cellular levels and abolishing all associated functions. PROTACs targeting enzymes in protein complexes disrupt both their catalytic activity and involvement in complex formation. In some cases, they also degrade other proteins in complexes, facilitating the elimination of entire assemblies. Our study leverages these unique features of TPD. We are currently developing various PROTACs targeting the enzymes responsible for lysine acetylation or methylation in proteins. Recently, the TPD concept has been extended beyond proteins to include nucleic acids, and ribonuclease-targeting chimeras (RIBOTACs) that selectively degrade RNA have been developed. We are also actively exploring new RNA-targeted degradation strategies. Herein, we highlight our recent work on TPD-inducing small molecules and provide an overview of RIBOTACs, which represent an area of growing research interest.

Targeted protein degradation (TPD), a technology that induces the degradation of a protein of interest (POI) by a chemical degrader, is a major trend in drug discovery research. Proteolysis targeting chimeras (PROTACs) are representative degraders that induce the ubiquitination of a POI, leading to its proteasomal degradation. Following the report of PROTAC efficacy in animals approximately a decade ago, TPD research continues to flourish. Unlike the occupancy-driven mechanism of traditional inhibitors, TPD employs an event-driven mechanism. Consequently, TPD is a highly anticipated technology capable of addressing therapeutic targets previously considered “undruggable.” Against this backdrop, our group is actively pursuing research focused on the targeted degradation of undruggable proteins. This symposium review summarizes our studies. It focuses on two distinct areas: the targeted degradation of aggregation-prone proteins for the development of neurodegenerative disorder treatments, and the targeted degradation of mitochondrial matrix-localized proteins for mitochondria-related diseases.

Structure-based drug design (SBDD) plays a crucial role in modern drug discovery. SBDD is a methodology that utilizes the three-dimensional (3D) structural information of a target protein to computationally search for compounds that bind to it and/or to optimize the binding of known compounds. This article provides an overview of recent advances in SBDD. Furthermore, we introduce 2 case studies conducted by the authors using single-particle analysis via Cryo-electron microscopy (Cryo-EM), a powerful technique for obtaining protein structures. The first example is the sodium ion (Na⁺)-translocating NADH-quinone oxidoreductase derived from Vibrio cholerae. This enzyme is suggested to undergo large conformational changes during the reaction cycle. By performing classification in single-particle analysis, we successfully captured a partial view of these conformational dynamics. The second example involves the angiotensin-converting enzyme 2 (ACE2) decoy, which binds to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and inhibits infection. Focusing on ACE2, which is critical for SARS-CoV-2 infection, an ACE2 decoy was developed to achieve higher binding affinity than the wild-type ACE2. We successfully elucidated how this ACE2 decoy binds to the spike protein.

ClpP protease is a highly conserved serine protease that plays a crucial role in bacterial protein quality control alongside its partner AAA+ ATPases. ClpP assembles into a barrel-shaped tetradecamer that degrades unfolded or misfolded proteins translocated by ATP-driven unfoldases, such as ClpC, ClpX, or ClpA. Acyldepsipeptide (ADEP) antibiotics bind to the hydrophobic pockets of ClpP, mimicking the natural interaction with ATPases, thus activating ClpP in an ATP-independent manner. ADEP binding induces major conformational changes that open the axial pores, enabling ClpP to degrade large protein substrates such as the cell division protein FtsZ, ultimately causing cell death. Our recent studies revealed that in Bacillus subtilis the ClpP proteolytic system regulates the intracellular levels of nonribosomal peptide synthetases SrfAA, SrfAB, and SrfAC, which are responsible for surfactin biosynthesis. Moreover, ADEP1-activated ClpP directly degraded SrfAA and SrfAB both in cells and in vitro, identifying new physiological substrates of the ADEP1–ClpP complex. High-speed atomic force microscopy (HS-AFM) analysis visualized the stepwise oligomerization of B. subtilis ClpP from monomers to heptamers and then to tetradecamers upon ADEP1 binding, revealing dynamic assembly processes underlying its activation. These findings enhance our understanding of bacterial protein degradation mechanisms and provide a molecular basis for the rational design of ClpP-targeting antibiotics with novel modes of action.

Amiodarone (AMD) is characterized by complex pharmacokinetics involving high lipophilicity and extensive protein binding. Serum AMD concentrations are influenced by triglyceride (TG) levels. Although the impact of TG on AMD concentrations at steady state has been previously investigated, data regarding the initial treatment period are limited. Given the prolonged half-life of AMD and the need for dose adjustments prior to reaching steady state, elucidating the effect of TG during this early phase is important. This retrospective study analyzed 64 patients who received AMD therapy at Sapporo City General Hospital between January 2016 and December 2024. Serum levels of AMD, its active metabolite desethylamiodarone (DEA), TG, and albumin were measured during the initial period (4–6 months) and steady-state period (7–12 months). Concentration-to-dose (C/D) ratios were calculated to assess pharmacokinetic variability during each period. Significant positive correlations were observed between serum TG levels and C/D_AMD during the initial (r=0.424, p<0.05) and steady-state (r=0.492, p<0.01) periods. A modest but significant correlation was observed between TG and C/D_DEA during the steady-state period (r=0.304, p<0.05). No significant correlations were found between albumin and C/D_AMD or C/D_DEA at any period. Serum TG levels affected AMD concentrations from the initial treatment period; however, the pharmacologically active unbound fraction remained stable. Consequently, dose adjustments based solely on fluctuations in TG levels are not required during the initial period. These findings contribute to the development of more precise AMD dosing strategies to maintain antiarrhythmic efficacy from treatment initiation.

In recent years, cancer chemotherapy has been administered in an outpatient setting; therefore, patient self-management of adverse events is an important issue. Pharmaceutical interventions were performed by pharmacists at the following 3 time points: before the physician consultation, after the physician consultation, and during multidisciplinary conferences at the Ibaraki Prefectural Central Hospital Cancer Chemotherapy Center. In this study, prescription proposals and their effectiveness for adverse events, were investigated. Of the 338 cases in which pharmaceutical interventions were performed, 280 were accepted by physicians, and the acceptance rates were 77% in conference, 89% before physician consultations, and 85% after physician consultations. Pharmaceutical interventions for the management of nausea and vomiting were most frequently accepted (96 cases), with improvement observed in 58 cases (60%). Improvement rates for hypertension and skin disorders were 76% and 56%, respectively, and improvement rates for peripheral neuropathy and dysgeusia were 33% and 22%, respectively. Of all interventions made by pharmacists, 68% were for the 1st 5 courses, with proposals continuing beyond the 6th course, suggesting that there is demand for long-term intervention. Pharmacists collecting patient information and implementing pharmaceutical interventions may contribute to the management of adverse events. As the degree of improvement varies according to the type of adverse event, it will be necessary to establish optimal pharmaceutical interventions in the future.

Equivalence of OTC formulations is generally assessed based on pharmaceutical attributes such as active ingredient content, dissolution behavior, and stability. However, for topical liquid formulations that are directly applied to the skin or scalp, the container design and usability may also influence the applied dose and the amount that reaches the target site. Appropriate design of containers or applicator devices is therefore essential for ensuring the effectiveness and safety of OTC topical products. In this study, we investigated the effects of container-tip geometry and hair density on scalp delivery of minoxidil (MXD) using four marketed MXD topical formulations. A scalp model was prepared by covering filter paper with human hair, and we evaluated: (1) the amount of MXD dispensed per actuation from each container, (2) the amount of MXD that reached beneath the hair layer, and (3) the in vitro skin permeation using porcine ear skin. Increased hair density reduced MXD delivery to the scalp for all formulations, especially for containers with larger tip ends. These findings suggest that ensuring the efficacy and reproducibility of MXD-containing OTC topical formulations requires not only optimizing drug permeability and formulation characteristics, but also considering hair density and container-tip geometry in designing appropriate usage conditions.