Peptide-based targeted protein degradation (TPD) has emerged as a transformative approach in drug discovery, enabling selective elimination of disease-associated proteins. This review summarizes advances in peptide-driven degradation technologies, covering ubiquitin-proteasome system-based strategies such as Peptide-based PROTACs (P-PROTACs) and hydrophobic tagging (HyT). It also highlights lysosome-targeting strategies-exemplified by lysosome-targeting chimeras (LYTACs)-that utilize the endocytosis-lysosome pathway for degrading extracellular and membrane proteins. Emerging autophagy-based approaches, including autophagosome-tethering compounds (ATTECs), further expand the degradable protein landscape. Additionally, peptide-based nanoself-assembly strategies are discussed as promising means to enhance targeting precision. The review covers fundamental principles, molecular design strategies, mechanisms, recent progress, and limitations of each platform. These innovations advance our understanding of cellular degradation pathways and offer promising therapeutic avenues for complex diseases, guiding the rational design and clinical translation of peptide-based degraders in next-generation precision medicine.

We designed pyrazolomorphinan derivatives as novel δ opioid receptor (DOR) selective agonists with an unprecedented chemotype according to the drug design concept for the DOR selective agonist KNT-127 which encompassed the message-address concept, the accessory site concept, and the conversion of an indole ring into a quinoline ring. The designed compounds as well as their regioisomers showed potent DOR agonistic activities with low or almost no activities for the μ (MOR) and κ opioid receptors (KOR). Among the tested compounds, SYK-1106 () bearing a cyclohexyl substituent was the most potent and efficacious DOR agonist (DOR: EC = 0.089 nM, = 111%; agonistic activities for the MOR and KOR were not determined). SYK-1106 showed dose-dependent and DOR antagonist NTI reversible antidepressant-like effects at 0.3 mg/kg, s.c. in the mouse forced-swimming tests without an effect on locomotor activity and with no convulsive effects.

Developing small-molecule colon-selective therapies for localized drug action is an attractive strategy in treating colonic diseases. Due to the lack of a reliable approach to understand human colon exposures, there have been few successful examples of clinically validated colon-targeted drugs. In this study, we aim to develop a physiologically based pharmacokinetic modeling approach that guides molecular design, formulation selection, and clinical trial design of small-molecule colon-selective therapies. We focus on the colon selectivity achieved through high hepatic extraction and modified release formulation, which are most likely to be predicted with confidence currently. With the established model, sensitivity analyses have identified compound and formulation design principles for achieving desirable colon-to-systemic selectivity. We have also demonstrated how the model can be used to guide first-in-human and late-stage clinical trials design. Overall, the established approach helps to facilitate rational drug design and clinical trial design for small-molecule colon-selective therapies.

Polo-like kinase 4 (PLK4) is a therapeutic target of high interest due to its essential role in mitotic regulation and centriole duplication. Recently, centriole depletion driven by PLK4 inhibition has been identified as a synthetically lethal target for cancers with elevated TRIM37 expression. Herein, we disclose the discovery of , a potent and selective PLK4 inhibitor. A validated hit from high-throughput screening of our compound library provided the starting point for further optimization. Structural analysis of multiple X-ray cocrystal structures enabled the design of analogs that demonstrated excellent kinome selectivity. Tumor regression was observed in efficacy studies of compound in a CHP-134 neuroblastoma xenograft tumor model.

Developing selective protease inhibitors is a challenging task due to the high structural resemblance of their catalytic pockets. Here, we aimed to develop selective inhibitors targeting TMPRSS6, a protease involved in regulating iron homeostasis. By exploiting structural differences in the catalytic subpockets between TMPRSS6 and matriptase, we optimized ketobenzothiazole-based peptidomimetics using the P4-P3-P2-Arg-Kbt scaffold. We found that a combination of bulky residues at P4 and P3, along with polar amino acids at P2, enhance selectivity while preserving high potency. Notably, WGU55 showed exceptional selectivity toward TMPRSS6 over matriptase and minimal off-target inhibition of coagulation serine proteases such as Factor Xa and Thrombin, representing, to our knowledge, the most selective TMPRSS6 inhibitor identified to date. Cell-based assays confirmed the inhibitor's high potency and selectivity. These findings validate a rational design strategy for the selective inhibition of TMPRSS6, paving the way for the development of targeted therapeutics based on peptidomimetics.

Inhibitors of cyclin-dependent kinases 4 and 6 have been shown to be clinically effective for the treatment of hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) advanced, or metastatic breast cancer. These agents, however, often show neutropenia, likely due to the role of CDK6 in hematopoiesis. Herein described is the discovery of a series of aminopyrimidine-based selective CDK4 inhibitors. Central to our strategy were efficiency-based optimization (LipE and LipMetE), structure-based drug design, and molecular dynamics simulation. The culmination of these efforts resulted in the discovery of PF-07220060 (atirmociclib), which possessed high potency and levels of selectivity for CDK4 over CDK6 that translated to minimal impact on neutrophils while driving efficacy in a mouse ZR75-1 xenograft model.

Boronic acid inhibitors often undergo nucleophilic addition upon binding to an enzyme due to the electrophilicity of the boron atom. A new class of boronic acid inhibitors of human phosphodiesterase 3B (PDE3B) has recently been disclosed, along with the 2.7 Å-resolution crystal structure of PDE3B complexed with inhibitor GSK4394835A [Rowley et al. (2024) Discovery and SAR study of boronic acid-based selective PDE3B inhibitors from a novel DNA-encoded library. , 2049-2065]. The crystal structure shows the binding of an intact, unreacted boronic acid, but discrepancies were evident in refinement statistics. Accordingly, we redetermined the structure using structure factor amplitudes deposited in the Protein Data Bank (accession code 8SYC), showing that the boronic acid moiety of GSK4394835A undergoes nucleophilic attack by H737 to form a tetrahedral boronate anion. We refined the structure to convergence with excellent refinement statistics, concluding that GSK4394835A is a reversible covalent inhibitor of PDE3B.

Muscle atrophy and cachexia are common comorbidities among patients suffering from cancer, chronic obstructive pulmonary disease, acquired immunodeficiency syndrome, and several other chronic diseases. The peptide hormone ghrelin exerts pleiotropic effects; it acts by stimulating growth hormone secretion and subsequent increase of insulin-like growth factor-1 levels, an important mediator of muscle growth and repair. Ghrelin also acts on inflammation, appetite, and adipogenesis and, therefore, has been considered a promising therapeutic target for catabolic conditions. We previously reported on the synthesis and properties of indane- and pyrrolidine-based series of ghrelin receptor full agonists, which led to a sustained increase of insulin-like growth factor-1 in a dog pharmacodynamic study. Herein, we report a subsequent lead optimization work that, taking advantage of the previous work on indanes and pyrrolidines, with the synthesis of only two dozen compounds, brought to the identification of compound suitable for progression as a clinical candidate.

Ubiquitin-specific protease 1 (USP1) represents an emerging therapeutic target for BRCA-deficient malignancies. Using a scaffold-hopping strategy derived from , we designed a novel series of USP1 inhibitors featuring a tricyclic core. Among them, two lead compounds and were identified with potent USP1 inhibitory and cellular antiproliferative activity. Further studies in MDA-MB-436 cells demonstrated that compounds and suppressed colony formation and induced S-phase arrest, with time- and concentration-dependently stabilizing ubiquitinated PCNA and amplifying -H2AX. Importantly, both compounds showed synergistic antiproliferative effects in combination with the PARP inhibitor Olaparib. Supported by its favorable pharmacokinetic properties, compound exhibited significant anticancer efficacy in an MDA-MB-436 xenograft model, achieving superior tumor growth inhibition both as monotherapy and in combination with Olaparib compared to . Collectively, compound emerges as a promising preclinical candidate with translational potential for BRCA-mutated breast cancer.

Peptide therapeutics are rapidly emerging as a new drug modality, bridging the gap between small molecules and biologics to target diseases such as diabetes, cancer, and cardiovascular disorders. Despite their advantages, challenges like metabolic instability, low permeability, and rapid clearance hinder their clinical development. This perspective focuses on addressing challenges in the metabolism of peptides by exploring key strategies including structural modifications (cyclization, incorporation of noncanonical amino acids, PEGylation, and lipidation) alongside advancements in delivery technologies (nanoparticles and protein conjugation). Low permeability and bioavailability of peptides are also briefly covered. Case studies, including semaglutide, MK-0616, LUNA18, sulanemadlin, and oxytocin analogs, illustrate successful applications of these strategies, highlighting how rational design and optimization have advanced peptide candidates from discovery to clinical stage.

Neuroinflammation is a key driver of Alzheimer's disease and an emerging therapeutic target. The p38/MK2 pathway regulates microglial cytokine production, yet previous attempts have not yielded modulators with clinically suitable properties. Here, we apply an integrative structure-guided and screening strategy to identify small-molecule disruptors of the p38/MK2 protein-protein interaction (PPI). Virtual screening of FDA-approved drugs prioritized nilotinib, a BCR-ABL inhibitor, as a putative PPI disruptor. Biochemical and molecular dynamics analyses confirmed that nilotinib binds to p38, blocks MK2 association, and suppresses cytokine release in microglia. Guided by these findings, we developed a lysate-based TR-FRET ultrahigh-throughput assay that identified additional inhibitors, including α-adrenergic antagonists doxazosin, terazosin, and alfuzosin. These compounds suppressed cytokine induction via docking groove blockade. Together, these results establish a non-ATP-competitive approach for selectively targeting the p38/MK2 complex and highlight the translational potential of drug repurposing to modulate neuroinflammation in Alzheimer's disease.

Radiolabeled fibroblast activation protein inhibitors (FAPIs) have emerged as promising diagnostic tracers for a wide range of cancers. The FAP trimer strategy has shown the potential to enhance both imaging and therapeutic efficacy in FAP-targeted applications. In this study, we designed and synthesized a novel trimeric linker to address existing limitations and improve the pharmacokinetic profile of FAPI-based probes. We developed and systematically evaluated a new FAP trimer based on the linker, Ga/Lu-DOTA-FAPI-FUSCC-Tri, for both diagnostic imaging and radioligand therapy. It demonstrated strong FAP-binding affinity (0.621 3.5 nM), enhanced tumor uptake (3.5 times), and significantly prolonged tumor retention time compared to monomeric counterparts, which showed a better improvement effect than similar linkers. Moreover, Lu-DOTA-FAPI-FUSCC-Tri highlights its potential as a dual-purpose agent for the integrated diagnosis and treatment of FAP-expressing tumors. This study identified a novel FAP trimer linker and successfully developed a high-performance FAP trimer based on it.

We report new anticonvulsant thiazolidine-2,4-diones with pendant benzenesulfonamide group that target epilepsy-associated carbonic anhydrase isoforms II and VII. Among these, , , , and exhibited remarkable inhibitory efficacy toward hCA II ( values of 4.1, 47.8, 9.6, and 6.9 nM, respectively) and hCA VII ( values of 9.4, 3.6, 41.6, and 98.3 nM, respectively), and selectivity over hCA I. was found to significantly reduce seizure severity and susceptibility, delay seizure onset, and lower seizure intensity in in vivo study of pilocarpine (PIL)-induced seizure model. Its superior in vivo stability and quick absorption were validated by pharmacokinetic studies. According to toxicological evaluations, there was no indication of neurotoxicity and a large safety margin (LD > 2000 mg/kg). According to mechanistic research, increased expression of KCC2 in the hippocampus, maintained neuronal integrity, and reduced mTOR activity. Molecular docking clarified interactions with hCA II and hCA VII.

Glycosylation is among the most common post-translational modifications of proteins. There is a great synthetic and practical difficulty in the assembly and deprotection of glycopeptides. State-of-the-art methods for glycopeptide synthesis are wasteful of glycosylated amino acids, are slow, and suffer from low yields. These shortcomings hamper accessibility to multiply glycosylated peptides. We report the accelerated, high-shear stirring-assisted synthesis of multiply -glycosylated peptides. The equimolar assembly was streamlined with deacetylation to provide multiglycosylated peptides at high purity. Cadherin-derived multiglycosylated peptides synthesized in large quantities provided selective electrochemical biosensing.

The phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is a critical regulator of cell growth and metabolism, and its dysregulation is implicated in various cancers. In this study, a series of dual-target degraders simultaneously targeting PI3K and mTOR was designed and synthesized. Compound was identified as a potent dual-degrader of both PI3K and mTOR, with DC values of 42.23-227.4 nM (PI3K) and 45.4 nM (mTOR) in MDA-MB-231 cells, also exhibited robust antiproliferative activity in multiple breast cancer cell lines. Mechanistic studies confirmed that achieved degradation through the ubiquitin-proteasome system (UPS). DIA proteomics and RNA-seq confirmed the on-target pathway modulation and revealed potential antileukemia activity. validation showed 's significant tumor growth suppression capability. These findings indicated that , as the first dual-targeted degrader of PI3K and mTOR, had great potential in the treatment of breast cancer and leukemia.

Despite the clinical success of tropomyosin receptor kinases (TRKs) inhibitors in fusion-positive cancers, prolonged administration has resulted in acquired resistance, particularly xDFG mutations, for which no approved therapies are available. Herein, we first presented a series of bifunctional agents as potent TRK inhibitors and degraders featuring a novel 5-amino-4-carbamoylpyrazole scaffold. The representative compounds and demonstrated potent antiproliferative activities against Ba/F3-LMNA-NTRK1 cells with IC values of 0.29 and 2.48 nM, respectively, and induced pronounced TRKA G667C degradation (DC = 5.86 and 24.69 nM; > 90%), while sparing the wild-type protein. Further assay displayed that effectively inhibited tumor growth with no apparent toxicity in the Ba/F3-LMNA-NTRK1 xenograft model. Overall, these findings indicated that, unlike conventional inhibitors, such bifunctional agents represent the first class of monovalent small molecules capable of effectively degrading TRK xDFG mutants, providing valuable insights into overcoming TRK xDFG-mediated clinical resistance.

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels mediating synaptic transmission at neuromuscular junctions and within both the central and peripheral nervous systems. The psychrophilic fungal tetrapeptide WvVf-OCH exhibits ∼55% inhibition of human muscle-type nAChR (hα1β1εδ) at 10 μM, suggesting potential for optimization. Structure-activity studies identified analogues, WrFr-OCH and WrFk-OCH, with significantly increased potency (75-90% inhibition at 1 μM) against hα1β1εδ nAChRs and, notably, the hα9α10 subtype. These analogues exhibit high-affinity binding through stable π-π stacking with the principal face and electrostatic interactions with the complementary face of the receptor binding site. Their unique alternating L/D chirality enhances proteolytic stability. , intravenous application of WrFr-OCH alleviated oxaliplatin-induced cold allodynia, while intramuscular injection reduced forelimb grip strength, consistent with muscle relaxant activity. Together, these findings identify WrFr-OCH as the shortest high-activity peptide ligand of human nAChRs reported to date, with therapeutic potential for both inflammatory pain management and muscle relaxation.

Proteasomes regulate cellular protein homeostasis and are key targets in treating cancer, inflammation, and autoimmune diseases. The two main forms, the constitutive proteasome and immunoproteasome, each contain three catalytically active subunits with distinct substrate specificities. The first approved proteasome inhibitor, bortezomib, is nonselective and causes dose-limiting toxicity. Herein, we report dipeptide boronic acids with varying P1 residues, prepared using our recently developed method for α-aminoboronic acids formation. Most compounds inhibited various immuno/proteasome subunits in the low nanomolar range, displaying inhibition profiles distinct from bortezomib, ranging from β5i/β1i-selective to β5c/β5i-directed inhibitors. Although their cytotoxicity to cancer cells was not improved compared to bortezomib, selected compounds proved less toxic to noncancer cells and with anti-inflammatory activity comparable to that of zetomipzomib (KZR-616). The presented boro dipeptides with tailored P1 residues provide a basis for designing subunit-selective compounds with boronic acid as the warhead and optimized P2 and/or P3 positions.

We discovered novel small molecule ligands of KLHDC2 and leveraged them to generate KLHDC2-mediated CDK6-selective degraders. Degrader exhibited potent and selective CDK6 degradation (DC = 0.037 μM) over CDK4 (DC > 10 μM) in MOLM-14 cells, leading to pronounced G/G cell-cycle arrest and apoptosis through inhibition of CDK6 downstream signaling. In addition, demonstrated superior growth-inhibitory activity compared to the warhead, palbociclib, in several leukemia cells and displayed favorable microsomal stability. Proteomic profiling confirmed that selectively degrades CDK6 with minimal effects on other CDK family members. Furthermore, reduced tumor burden and CDK6 levels in an in vivo xenograft model. Collectively, these findings highlight the potential of KLHDC2-mediated degraders as a novel strategy for selective CDK6 degradation and underscore the promise of KLHDC2 as an alternative E3 ligase platform for targeted protein degradation.

Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is highly upregulated in multiple cancers and serves as a promising biomarker for patient staging and therapy guidance. We designed five ROR1-targeted radiotracers, including linear and cyclic peptides derived from PR7, and evaluated their specificity and affinity in vitro and in vivo. All probes showed a rapid tumor uptake within 30 min in MC38 models. Saturation binding assays and blocking studies confirmed the ROR1 specificity. Positron emission tomography imaging with [Ga]Ga-DP1 and [F]AlF-NP1 demonstrated excellent tumor targeting and favorable target-to-nontarget ratios across multiple models, with renal clearance observed in biodistribution. Transcriptomic analysis indicated the potential involvement of ROR1 in the PI3K/AKT pathway. In general, these findings support [F]AlF-NP1 and [Ga]Ga-DP1 as promising noninvasive imaging agents for quantitative ROR1 visualization and personalized cancer therapy.