Here, we report three classes of dipicolinic acid (Dipic)-stabilized diaminobis(phenolato) Zr -chelates with high aqueous stability and potent antiproliferative activity. Among them, complex exhibited strong cytotoxicit...Here, we report three classes of dipicolinic acid (Dipic)-stabilized diaminobis(phenolato) Zr -chelates with high aqueous stability and potent antiproliferative activity. Among them, complex exhibited strong cytotoxicity against multiple cancer cell lines, including cisplatin-resistant Hep G2/DDP cells, while showing low toxicity toward normal LO2 cells. Mechanistic studies demonstrated that preferentially accumulates in mitochondria and lysosomes, leading to excessive ROS generation, lipid peroxidation, mitochondrial membrane depolarization, and GPX4 downregulation, consistent with ferroptosis induction. Concurrently, lysosomal iron accumulation, membrane permeabilization, and CTSB/caspase-8 activation indicated the involvement of lysosome-dependent cell death, further exacerbating oxidative stress. Moreover, triggered immunogenic cell death and activated cGAS-STING signaling. , significantly suppressed tumor growth in a Hep G2/DDP xenograft model with minimal systemic toxicity, highlighting Dipic-stabilized Zr -chelates as promising candidates for the treatment of chemoresistant cancers.
Tumor-associated carbonic anhydrases (hCA IX and XII) drive cancer survival under hypoxia. However, developing therapeutics that avoid the ubiquitous physiological isoforms (hCA I and II) to prevent off-target liabilitie...Tumor-associated carbonic anhydrases (hCA IX and XII) drive cancer survival under hypoxia. However, developing therapeutics that avoid the ubiquitous physiological isoforms (hCA I and II) to prevent off-target liabilities remains challenging. Herein, we report the design, synthesis, and evaluation of novel 3,4-dihydroquinazoline-based benzenesulfonamides as selective hCA inhibitors. Structure-activity relationship and molecular dynamics studies demonstrated that converting primary amines to imine derivatives successfully abolished hCA I activity while retaining nanomolar potency against hCA IX and XII. Specifically, BE21349 showed high affinity for hCA IX ( = 61.8 nM) and hCA XII (= 40.5 nM), exhibiting over 33- and 51-fold selectivity for these respective isoforms over hCA I ( = 2090 nM). Antiproliferative screening identified the hCA I-inactive derivatives BE21349 and BE21417 as potent multitarget agents across the NCI-60 panel. Notably, BE21417 exhibited a nearly 6-fold preference for hCA XII over hCA II, representing a promising targeted anticancer scaffold.
B-cell lymphoma 6 (BCL6) is a transcriptional repressor implicated in diffuse large B-cell lymphoma and other malignancies. Conventional BCL6 inhibitors and degraders rely on loss-of-function mechanisms that may be limit...B-cell lymphoma 6 (BCL6) is a transcriptional repressor implicated in diffuse large B-cell lymphoma and other malignancies. Conventional BCL6 inhibitors and degraders rely on loss-of-function mechanisms that may be limited by incomplete pathway suppression. Transcriptional chemical inducers of proximity (TCIPs) provide a gain-of-function alternative by redirecting transcriptional coactivators to BCL6-bound genomic loci, thereby reactivating pro-apoptotic gene expression. Here, we describe the medicinal chemistry optimization of BCL6 TCIPs through systematic linker engineering. A focused library of 66 heterobifunctional analogues derived from JQ1 and BI-3812 was evaluated for ternary complex formation, cellular potency, and selectivity. Linker rigidification and incorporation of cyclic elements significantly improved cellular selectivity, enhanced solubility, and increased the plasma exposure in mice. Computational analyses, competition experiments, and RNA sequencing indicate that the effects of the optimized analogues are driven by ternary complex formation. Together, these findings establish the linker architecture as a critical determinant of TCIP performance.
Fibroblast activation protein (FAP) is an important target for tumor diagnosis and therapy. In this study, two FAP-targeted radioligands, the monomeric [Ga]Ga-DOTA-T1-FAPI and the dimeric [Ga]Ga-DOTA-T1-(FAPI), were desi...Fibroblast activation protein (FAP) is an important target for tumor diagnosis and therapy. In this study, two FAP-targeted radioligands, the monomeric [Ga]Ga-DOTA-T1-FAPI and the dimeric [Ga]Ga-DOTA-T1-(FAPI), were designed by introducing a glucose linker into FAPI-04 and its dimer, and their FAP-targeting capability was further evaluated. In vitro studies demonstrated that [Ga]Ga-DOTA-T1-(FAPI) exhibited specific uptake in FAP-positive U87 MG cells. Small animal positron emission tomography and computed tomography (PET/CT) imaging and biodistribution studies showed that the dimeric tracer exhibited higher tumor uptake (9.5 ± 1.75% ID/g at 30 min) and superior tumor-to-nontarget ratios compared with [Ga]Ga-DOTA-T1-FAPI (3.02 ± 0.19% ID/g at 30 min) and [Ga]Ga-DOTA-FAPI-04 (1.44 ± 0.34% ID/g at 30 min). Furthermore, [Lu]Lu-DOTA-T1-(FAPI) displayed high tumor uptake (10.83 ± 1.92% ID/g at 4 h) and favorable imaging contrast. Overall, the combination of glycosylation and dimerization provides a promising strategy for developing efficient FAP-targeted diagnostic and therapeutic radioligands.
Metastatic castration-resistant prostate cancer remains difficult to treat because conventional small-molecule therapies often lack tumor selectivity and have limited effective exposure. Sorafenib is a multikinase inhibi...Metastatic castration-resistant prostate cancer remains difficult to treat because conventional small-molecule therapies often lack tumor selectivity and have limited effective exposure. Sorafenib is a multikinase inhibitor that suppresses RAF-MEK-ERK signaling and angiogenesis, but its poor aqueous solubility limits its use. Here, we developed a prostate-specific membrane antigen (PSMA)-targeted poly(amidoamine) dendrimer-sorafenib conjugate, PD-Sora-CTT1298, using sequential CuAAC and SPAAC chemistry. The conjugate showed reproducible composition, high aqueous solubility, nanoscale size, and formulation stability. PD-Sora-CTT1298-Cy5 showed time-dependent PSMA-associated internalization in VCaP and PC3-PIP cells, with limited uptake in PSMA-negative DU145 cells. In VCaP cells, PD-Sora-CTT1298 produced greater in vitro suppression of viability, proliferation, MAPK signaling, VEGF-A secretion, endothelial tube formation, and autophagic vesicle accumulation than did free sorafenib. Combination with olaparib further reduced viability and increased apoptotic signaling. These findings support the further preclinical evaluation of PSMA-targeted dendrimer delivery for sorafenib-based prostate cancer therapy.
Hydrolytic drug-metabolizing enzymes (hydrolases) are essential for the metabolism of many therapeutic agents; however, comprehensive data on their tissue distribution and interspecies variability remain limited. To addr...Hydrolytic drug-metabolizing enzymes (hydrolases) are essential for the metabolism of many therapeutic agents; however, comprehensive data on their tissue distribution and interspecies variability remain limited. To address this knowledge gap, the primary objective of this study was to quantify the abundance of drug metabolism-relevant hydrolases (e.g., CES1/2, PON1/2/3, BPHL, APEH, CMBL, EPHX1/2, DPP4, and AADAC) across liver, intestine, and kidney tissues in humans, rats, mice, dogs, and monkeys using a comprehensive global proteomics approach. Further, we present here qualitative and quantitative differences in intertissue and interspecies variability among 182 detected hydrolases. Humans exhibited the greatest variability of hydrolases across tissues, with marked qualitative and quantitative differences in protein abundance observed between species. Orthology analysis highlighted substantial sequence conservation in monkeys but greater divergence in rodents and dogs. Overall, these findings could provide critical quantitative data to inform animal model selection and improve the translation of preclinical drug metabolism studies to humans for drugs that are majorly metabolized by hydrolases.
The recent clinical success of macrocyclic peptides, such as bremelanotide and setmelanotide, highlights the potential of this modality as a "Goldilocks" chemical class, effectively balancing the properties of small mole...The recent clinical success of macrocyclic peptides, such as bremelanotide and setmelanotide, highlights the potential of this modality as a "Goldilocks" chemical class, effectively balancing the properties of small molecules and biologics while optimizing their affinity, stability, and pharmacokinetics. Despite their potential, achieving selective MCR targeting with optimal pharmacological profiles remains challenging. Motivated by these considerations, we designed and synthesized a series of 14 macrocyclic peptide analogs (19-23-membered rings) based on , , and scaffolds. Their pharmacological activities were assessed using human MC1R, MC3R, MC4R, and MC5R. The novel macrocyclic compounds and emerged as potent and selective MC4R antagonists. Additionally, exhibited interesting agonist activity with remarkable selectivity for the same receptor. This study underscores the potential of tailored midsized macrocycles as selective MCR ligands and provides new insights into the structure-activity relationships, thereby guiding the development of therapeutic candidates for metabolic and inflammatory diseases.
Cell-based therapies have transformed the treatment landscape for cancer, yet their clinical translation remains limited by unpredictable in vivo behavior and variable patient responses. Accurate, noninvasive image-based...Cell-based therapies have transformed the treatment landscape for cancer, yet their clinical translation remains limited by unpredictable in vivo behavior and variable patient responses. Accurate, noninvasive image-based tracking of therapeutic cells, such as PET/CT, is essential for understanding biodistribution, improving safety, and optimizing the design of next-generation treatments. However, existing radiolabeling strategies for cell tracking using PET/CT lack the stability and sensitivity required for reliable long-term imaging. Here, we present a direct radiolabeling strategy that oxidizes cell surface sialic acids to conjugate aminooxy-DFO (AOD) and subsequently radiolabels cells with Zr under biocompatible conditions. We radiolabeled five human and nonhuman primate immune cell types with high radiochemical incorporation (17-194 μCi per million cells) and purity (∼90%), while preserving cell viability. Serial PET/CT imaging over 7-8 days revealed conserved biodistribution patterns across all cell types tested. This approach provides a robust, applicable platform for longitudinal PET/CT tracking of therapeutic cells.
Human carbonic anhydrase IX (hCA IX) is markedly overexpressed in clear cell renal cell carcinoma and plays a key role in establishing an acidic tumor microenvironment associated with intrinsic chemoresistance. Extracell...Human carbonic anhydrase IX (hCA IX) is markedly overexpressed in clear cell renal cell carcinoma and plays a key role in establishing an acidic tumor microenvironment associated with intrinsic chemoresistance. Extracellular acidification limits the uptake and efficacy of several cytotoxic agents, including bendamustine, a bifunctional alkylating agent whose activity depends on intracellular accumulation and DNA cross-link formation. Herein, we report the design and synthesis of novel bendamustine-carbonic anhydrase inhibitor (CAI) hybrids aimed at combining CA IX targeting with DNA-damaging activity. Structural modification of the bendamustine butyric acid side chain enabled the introduction of CAI warheads while preserving the alkylating moiety. The resulting compounds were evaluated against hCA I, II, IX, and XII, displaying preferential inhibition of the tumor-associated isoforms. Selected derivatives ( and ) showed antiproliferative activity in 786-O and CAKI-1 cells, inducing cell-cycle arrest and reducing long-term proliferative capacity more effectively than the reference CA IX inhibitor SLC-0111.
Acute liver injury (ALI) is a rapidly progressive inflammatory disease lacking precise noninvasive early diagnostic tools, as traditional enzyme-based tests frequently yield false-positive results. Polarity is a crucial...Acute liver injury (ALI) is a rapidly progressive inflammatory disease lacking precise noninvasive early diagnostic tools, as traditional enzyme-based tests frequently yield false-positive results. Polarity is a crucial physiological indicator, and its abnormal fluctuations are deeply involved in ALI pathogenesis, necessitating accurate in vivo monitoring. We rationally designed , a new near-infrared ratiometric fluorescent probe featuring a D-π-A architecture for highly sensitive polarity detection. It possesses excellent vesicle-targeting capabilities, enabling precise tracking of polarity dynamics within lipid droplets during ALI progression. With exceptional photostability, low cytotoxicity, and ratiometric signal output that effectively eliminates background interference, achieves accurate real-time imaging of polarity variations in live cells, zebrafish, and mice. Furthermore, we successfully utilized it as an optical platform to screen anti-inflammatory natural products. This work provides a robust noninvasive tool for dynamic polarity monitoring, early ALI diagnosis, and high-throughput drug discovery.
Rifamycins are a cornerstone of antimycobacterial therapy. However, their clinical use is limited by drug-drug interactions, arising from activation of the nuclear receptor pregnane X receptor (PXR). PXR activation induc...Rifamycins are a cornerstone of antimycobacterial therapy. However, their clinical use is limited by drug-drug interactions, arising from activation of the nuclear receptor pregnane X receptor (PXR). PXR activation induces expression of drug-metabolizing enzymes, including the cytochrome P450 3A4 isoform (CYP3A4), and accelerates clearance of coadministered medications. The structural understanding of rifamycin-PXR interactions remains limited. We designed a series of C25-modified rifabutin analogs and systematically evaluated their PXR binding, transcriptional activation, and pharmacological profile. Several analogs retained PXR binding affinity yet showed reduced CYP3A4 induction, exhibiting behavior consistent with antagonists or inverse agonists and revealing a disconnect between receptor binding and transcriptional activation. Molecular dynamics simulations indicated C25 modifications may disrupt positioning of the PXR α12 helix through steric interactions. These findings demonstrate conservative modifications of rifamycin can potentially convert PXR agonists into antagonists or inverse agonists and offer a structure-guided framework for developing rifamycins with attenuated CYP3A4 induction.
Selective targeting SMARCA2 by degradation represents a promising new therapeutic strategy for human cancers harboring deficient SMARCA4. Herein we report the discovery of highly potent, selective and oral available SMAR...Selective targeting SMARCA2 by degradation represents a promising new therapeutic strategy for human cancers harboring deficient SMARCA4. Herein we report the discovery of highly potent, selective and oral available SMARCA2 PROTAC degraders, as exemplified by SMD-6346. SMD-6346 achieves DC = 3.3 nM and > 90% against SMARCA2 and only modest activity against SMARCA4 (DC > 1000 nM, = 46%). SMD-6346 potently and effectively inhibits cell growth in SMARCA4-deficient cancer cell lines and displays minimal cell growth inhibition activity in SMARCA2/4 wild-type cancer cell lines. SMD-6346 attains an excellent pharmacokinetic profile and 61% oral bioavailability in mice. Daily oral administration of SMD-6346 induces robust SMARCA2 depletion in tumor tissues in mice and significantly inhibits tumor growth in the H838 SMARCA4-deficient xenograft model in mice. SMD-6346 is a promising, orally bioavailable SMARCA2 degrader for further optimization for the development of a new therapy for SMARCA4-deficient human cancers.
Cyclin-dependent kinase 2 (CDK2) represents a critical therapeutic target in tumors resistant to CDK4/6 inhibitors or with amplification. However, selective inhibition of CDK2 remains challenging owing to the high struc...Cyclin-dependent kinase 2 (CDK2) represents a critical therapeutic target in tumors resistant to CDK4/6 inhibitors or with amplification. However, selective inhibition of CDK2 remains challenging owing to the high structural homology among CDKs. In this study, we identify and as cereblon (CRBN)-based molecular glue degraders that selectively degrade CDK2. Ternary complex structures reveal a noncanonical recruitment mode centered on CDK2 Glu57, which bypasses the canonical G-loop/β-hairpin and kinase glycine-rich loop interactions and is stabilized by an extended CRBN-CDK2 interface. Mechanistically, these degraders inhibit retinoblastoma (Rb) phosphorylation and induce G1/S-phase arrest, suppressing CDK2-dependent cell proliferation. further exhibits improved pharmacokinetics, measurable oral bioavailability, and target engagement, achieving intratumoral CDK2 degradation following intraperitoneal administration. Collectively, this study provides a structural blueprint for designing selective kinase degraders and establishes B12 as a chemically tractable probe for targeting CDK2-driven malignancies.
NLRP3 inflammasome is a critical cytosolic multiprotein complex central to the innate immune response. Upon activation, NLRP3 oligomerizes and recruits the adapter protein ASC; this scaffold recruits and activates pro-ca...NLRP3 inflammasome is a critical cytosolic multiprotein complex central to the innate immune response. Upon activation, NLRP3 oligomerizes and recruits the adapter protein ASC; this scaffold recruits and activates pro-caspase-1. Active caspase-1 catalyzes the proteolytic maturation and secretion of the potent pro-inflammatory cytokines IL-1β and IL-18, and induces a programmed cell death called pyroptosis. Dysregulated or chronic NLRP3 inflammasome activation is a major driver of pathogenesis in a wide spectrum of peripheral inflammatory diseases, including gout, pericarditis, atherosclerosis, nonalcoholic steatohepatitis, and NLRP3 gain-of-function autoinflammatory disorders known as CAPS, as well as neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. Herein we described the discovery of NLRP3 inhibitors based on the [1,2,4]triazolo[1,5-]pyrimidine scaffold. Represented by compound , this scaffold exhibited exceptional potency, favorable physicochemical properties, and desirable pharmacokinetic profiles, including good brain penetration. Compound showed potential as a candidate for the treatment of Parkinson's disease.
The natural antifungal peptide Histatin 5 (Hst 5) is a histidine-rich cationic peptide secreted by human salivary glands and a key component of oral innate immunity, but its moderate activity limits clinical use. Hst 5 e...The natural antifungal peptide Histatin 5 (Hst 5) is a histidine-rich cationic peptide secreted by human salivary glands and a key component of oral innate immunity, but its moderate activity limits clinical use. Hst 5 enters via the membrane receptor Ssa1/2. Here, we integrated artificial intelligence-assisted and computer-aided drug design to rationally modified the sequence structure of Hst 5. Truncated derivatives of Hst5 were screened for antimicrobial potential using ESM2-AFPpred, and high-probability candidates were docked with Ssa1/2. The Hst 5-22 was identified, then redesigned based on alanine scanning to yield the optimized derivative Hst 5-22-RW. Compared with Hst 5, Hst 5-22-RW has a shorter sequence, stronger Ssa1/2 binding, and improved activity against . It also shows superior activity against fluconazole-resistant strains. RT-qPCR and transmembrane tracking confirmed higher cellular transport efficiency in . The CADD/AIDD-driven optimization successfully generated the highly active antifungal peptide Hst 5-22-RW, providing a novel strategy for rational modification of antimicrobial peptides.
Tyagi M, Poongavanam V, Zich S
… +11 more, Lindhagen M, Asproudis I, Putra OD, Yang J, Ashworth ZJR, Guadagni A, Hagemeyer LJ, Oliva A, Sjö P, Schiesser S, Kihlberg J
Macrocycles are a highly interesting modality to modulate difficult-to-drug targets, but often reside in chemical space where obtaining sufficient cell permeability and solubility is challenging. We have determined perme...Macrocycles are a highly interesting modality to modulate difficult-to-drug targets, but often reside in chemical space where obtaining sufficient cell permeability and solubility is challenging. We have determined permeability across Caco-2 cells, aqueous solubility and log for four series of semipeptidic macrocycles and one series of linear matched molecular pairs. By using X-ray crystallography, NMR spectroscopy, and computational chemistry, unexpected permeability differences between series and matched pairs were explained by differences in conformational preferences that determine the formation of intramolecular interactions. Macrocycles that formed intramolecular NH-π interactions and hydrogen bonds were more permeable than matched pairs unable to form such interactions. The elevated permeability of linear compounds was concluded to result from their greater conformational flexibility, allowing them to shield amide bonds and expose nonpolar groups to a greater extent than their macrocyclic matched pairs. Solubility was less dependent on specific intramolecular interactions and was predominantly low at log >2.5.
Parkinson's disease (PD) is a multifactorial neurodegenerative disorder for which single-target therapeutic strategies have shown limited success. To address this challenge, we pursued a structure-based polypharmacologic...Parkinson's disease (PD) is a multifactorial neurodegenerative disorder for which single-target therapeutic strategies have shown limited success. To address this challenge, we pursued a structure-based polypharmacological approach targeting both the hyperactive G2019S mutant of leucine-rich repeat kinase 2 (LRRK2) and c-Jun N-terminal kinase 3 (JNK3), two kinases implicated in PD pathogenesis. Virtual screening, design, and biological evaluation identified -phenyl-9-purine-2,6-diamine (NPPD)-based scaffolds as promising dual-target hits. Subsequent macrocyclization and systematic structure-activity relationship optimization led to inhibitors with improved potency and drug-like properties. Among these, compound exhibited low-nanomolar enzymatic inhibition against both kinases and exceptional picomolar cellular potency against LRRK2. While optimal cellular activity against JNK3 remains challenging, compound demonstrated a favorable kinome-wide selectivity profile. Pharmacokinetic studies revealed excellent oral exposure, moderate clearance, and efficient brain penetration without observable toxicity. Overall, this study identifies a promising lead compound with significant potential as a therapeutic agent for PD.
Drug-induced liver injury (DILI) is a leading cause of drug failure and post-market withdrawals. Traditional preclinical methods fail to detect up to 40-45% of clinical hepatotoxicity cases. Computational approaches, par...Drug-induced liver injury (DILI) is a leading cause of drug failure and post-market withdrawals. Traditional preclinical methods fail to detect up to 40-45% of clinical hepatotoxicity cases. Computational approaches, particularly those based on machine learning and deep learning (DL), are emerging as promising tools to support medicinal chemistry and early drug discovery, though their predictive capabilities remain under active investigation. In this perspective, we review the development of DILI annotation data sets, tracing their growth from small collections to large, comprehensive resources. We also outline the evolution of computational methods, from simple descriptor-based models to advanced DL and ensemble approaches that incorporate interpretable features. Finally, we highlight recent efforts to integrate standardized causality frameworks, pharmacogenomics, and mechanistic models, aiming to connect computational advances with clinical relevance. This perspective provides valuable insight for researchers and promotes the development of more robust and consensual DILI prediction strategies.