Small molecules, big impact: 20 years of targeted therapy in oncology

Identification and characterization of Bufalin as a novel EGFR degrader

Esophageal squamous cell carcinoma (ESCC) stands out as a common cancer type worldwide, characterized by its notably high rates of occurrence and mortality. The epidermal growth factor receptor (EGFR) is one of the main targets for cancer treatment as it is one of the genes whose expression is often altered by overexpression, amplification, and mutation in a variety of solid tumors. Substantial efforts have been made to develop EGFR-targeted therapeutic agents, including monoclonal antibodies and tyrosine kinase inhibitors (TKIs). However, these agents exhibited limited efficacy due to the emergence of acquired resistance. Therefore, novel treatment strategies targeting EGFR are urgently needed. Recent studies have identified a few natural compounds that can efficiently inhibit EGFR, indicating that natural products may be potential sources for the development of new EGFR inhibitors. Here, using the Drug Affinity Responsive Target Stability (DARTS) assay combined with liquid chromatography/tandem mass spectrometry analysis, co-crystal method, we discovered that Bufalin directly interacts with EGFR and causes EGFR endocytosis and degradation in the lysosome. Moreover, Bufalin exhibits superior anti-tumor activity compared with another EGFR TKIs. Our study identified Bufalin as the first natural small-molecule EGFR degrader, which suppresses EGFR signaling by inducing the degradation of EGFR via the endosome-lysosome pathway.

CD36-mediated endocytosis of proteolysis-targeting chimeras

Passive diffusion does not explain why many drugs are too large and/or too polar for rule-breaking membrane penetration, such as proteolysis-targeting chimeras (PROTACs, generally of a molecular weight > 800 Da). Here, using biotinylated chemical-probe-based target fishing and genetic knockdown/knockin approaches, we discovered that the membrane cluster of differentiation 36 (CD36) binds to and facilitates the uptake and efficacy of diverse PROTACs (e.g., SIM1-Me, MZ1, and clinical ARV-110) and large and/or polar small-molecule drugs (e.g., rapalink-1, rapamycin, navitoclax, birinapant, tubacin, and doxorubicin) via the CD36-mediated early endosome antigen 1 (EEA1)/Ras-related protein 5A (Rab5) endosomal cascade in vitro and/or in vivo. We then devised a novel chemical endocytic medicinal chemistry strategy to improve binding of PROTACs to CD36 using structural modifications via the prodrug approach, markedly enhancing PROTAC anti-tumor efficacy through spontaneously augmenting permeability and solubility.

Advancements in delivery Systems for Proteolysis-Targeting Chimeras (PROTACs): Overcoming challenges and expanding biomedical applications

PROTAC (Proteolysis-Targeting Chimera), an emerging drug development strategy based on small molecule technology, has garnered widespread attention due to its high efficiency, broad applicability, low resistance, and dosage advantages. However, PROTAC molecules still exhibit certain limitations that require urgent resolution. Although significant progress has been made in designing PROTACs that target various disease-related proteins, research on drug delivery systems (DDS) for PROTACs remains relatively limited. This review aims to explore the critical role of delivery system design in addressing the inherent challenges associated with PROTAC molecules from a novel perspective. Beginning with five major challenges-insufficient targeting, poor pharmacokinetic properties, low cell permeability, limited accessibility, and the Hook effect-this article introduces formulation strategies to mitigate these deficiencies. It discusses potential solutions through targeted modifications, nano-delivery systems, intelligent response systems, and membrane biomimetic technologies, among others. Furthermore, it elucidates the mechanisms and principles underlying these approaches and analyzes the advantages of various delivery strategies. The insights provided in this review offer insights for designing delivery systems tailored to PROTACs with diverse characteristics for different disease applications.

Design, synthesis, and biological evaluation of novel PI3Kδ/HDAC6 dual inhibitors for the treatment of non-Hodgkin's lymphoma

PI3Kδ and HDAC6 inhibitors play important roles in the treatment of lymphoma. Herein, a novel series of purine-based PI3Kδ/HDAC6 dual inhibitors have been rationally designed and synthesized by incorporating an HDAC pharmacophore into our previously reported PI3Kδ inhibitor scaffold. Structure-activity relationship (SAR) studies led to the discovery of the lead compound 22E, which showed potent inhibitory activity towards PI3Kδ and HDAC6, with IC50 values of 2.4 nM and 6.2 nM, respectively. Compound 22E showed significantly enhanced antiproliferative activities against multiple non-Hodgkin's lymphoma (NHL) cells compared with either selective PI3Kδ inhibitor or HDAC6 inhibitor, with IC50 values of 34 nM and 53 nM against SU-DHL-6 and JEKO-1 cells, respectively. Subsequent mechanistic studies revealed that compound 22E effectively arrested the cell cycle in the G0/G1 phase and induced cell apoptosis in SU-DHL-6 and JEKO-1 cells. Meanwhile, 22E could simultaneously block the PI3K/AKT/mTOR signaling pathway as well as increase the acetylation of α-tubulin and histone H3 levels. In addition, 22E prevented tumor growth in both SU-DHL-6 and JEKO-1 xenograft models, and there was no observable toxicity. These results demonstrated that 22E is a promising lead candidate with novel antitumor mechanism for the treatment of NHL.

CD44-targeted virus-mimicking nanomedicine eliminates cancer stem cells and mitigates chemoresistance in head and neck squamous cell carcinoma

Cancer stem cells (CSCs) play critical roles in tumor growth, metastasis, and chemoresistance. Although several small-molecule inhibitors designed to inhibit CSCs have been investigated in clinical trials, their inadequate tumor targeting and potential off-target side effects have led to poor outcomes. A CD44-targeted virus-mimicking nanomedicine encapsulating the BMI1 inhibitor PTC209 (PTC209@VNP-HA) was designed to treat head and neck squamous cell carcinoma (HNSCC). We used a dendritic mesoporous silica nanoparticle (MSN) as the core for virus-mimicking nanoparticle (VNP) formation after adding shell particles to the MSN surface. The VNP surface was then modified with hyaluronic acid (HA), and PTC209 was adsorbed by mesopores to form PTC209@VNP-HA. In this system, HA is used to target CD44+ CSCs. The rough surface of VNP-HA provided better drug delivery efficiency than smooth nanoparticles modified with HA. VNP-HA enhanced the cancer inhibitory effect of PTC209 12-fold compared to the administration of free PTC209, leading to significantly higher bioavailability of PTC209. Both in vitro and in vivo assays showed that PTC209@VNP-HA inhibited cancer stemness, proliferation, and metastasis in HNSCC. Mechanistically, this inhibitory effect is closely associated with DNA damage/apoptosis signaling. Using a series of preclinical models in murine systems, we confirmed that PTC209@VNP-HA eliminated BMI1+ CSCs, and greatly inhibited the proliferation and metastasis of HNSCC when combined with cisplatin. This study investigated PTC209@VNP-HA as a novel and potentially transformative HNSCC treatment option that eliminates CSCs, prevents metastasis, and overcomes cisplatin resistance.

Protacs in cancer therapy: mechanisms, design, clinical trials, and future directions

Cancer develops as a result of changes in both genetic and epigenetic mechanisms, which lead to the activation of oncogenes and the suppression of tumor suppressor genes. Despite advancements in cancer treatments, the primary approach still involves a combination of chemotherapy, radiotherapy, and surgery, typically providing a median survival of approximately five years for patients. Unfortunately, these therapeutic interventions often bring about substantial side effects and toxicities, significantly impacting the overall quality of life for individuals undergoing treatment. Therefore, urgent need of research required which comes up with effective treatment of cancer. This review explores the transformative role of Proteolysis-Targeting Chimeras (PROTACs) in cancer therapy. PROTACs, an innovative drug development strategy, utilize the cell's protein degradation machinery to selectively eliminate disease-causing proteins. The review covers the historical background, mechanism of action, design, and structure of PROTACs, emphasizing their precision in targeting oncogenic proteins. The discussion extends to the challenges, nanotechnology applications, and ongoing clinical trials, showcasing promising results and clinical progress. The review concludes with insights into patents, future directions, and the potential impact of PROTACs in addressing dysregulated protein expression across various diseases. Overall, it provides a concise yet comprehensive overview for researchers, clinicians, and industry professionals involved in developing targeted therapies.

Programmable Transcriptional-Translation Active Sensors for miRNA-Responsive Gene Imaging and Theranostics in Mammalians

Synthetic gene circuits are logical circuits constructed by various biological elements based on engineering principles. However, the majority of current synthetic gene circuits are modulated through exogenous factors or endogenous inhibitory substances, which results in redundant structures and low efficiency, thereby greatly limiting their application scenarios. In this study, we developed a miCU sensor system comprising the Gal4-VP16 gene element, which enables real-time targeted monitoring of miR-9 and miR-124a during neural differentiation through transcriptional-translation two-step active regulation with a relatively low background signal. Additionally, the functional gene was replaced by P21 through the programmability of miCU, thereby achieving miRNA-mediated cell cycle arrest and suppression of cell migration in tumor cells. Furthermore, by strategically substituting the target miRNA with miR-155 and concurrently introducing the therapeutic gene Nrf2 into the miCU system, the integration of disease diagnosis and treatment in lipopolysaccharide (LPS)-induced acute liver injury (ALI) mouse models has been successfully achieved. Our study presented a programmable miRNA-responsive gene regulation platform, which may offer a robust tool for precise diagnosis and treatment in disease settings.

Improvement of Drug Release from an Aptamer Drug Conjugate Using Reductive-sensitive Linkers for Tumor-targeted Drug Delivery

The selective delivery of small molecule compounds such as Gemcitabine to tumor cells is a promising methodology for enhancing therapeutic efficacy and attenuating the side effects of anticancer drugs. Aptamers are useful as target-directed ligands for tumor-selective drug delivery due to their ability to bind specific proteins. However, the drug must be released from the aptamer after the conjugate is taken up by the cell to exert its pharmacological effect. In this study, we designed and synthesized a conjugate in which a linker cleaved by glutathione, which is highly expressed in tumor cells, was inserted between the aptamer (AS1411) and Gemcitabine. Almost all Gemcitabine was released from the conjugate after 30 min in the presence of 6 mM glutathione. AS1411 is known to bind to nucleolin, which is highly expressed on tumor cells. The cytotoxicity of the AS1411 and Gemcitabine conjugate with a disulfide bond on A549 cells was higher than that of the conjugate without a disulfide bond. Furthermore, the cytotoxicity of the disulfide-linked conjugate of AS1411 and Gemcitabine was higher in A549 cells than in MCF10A cells, which were used as the model of normal cells. These results indicate that disulfide conjugation enhanced the tumor cell-selective cytotoxicity of Gemcitabine with AS1411.

Advances in the diagnosis and treatment of urethral metastasis after urothelial carcinoma surgery: A case series and literature review of 3 total ureterectomy cases

RATIONALE

Urethral metastasis recurrence after surgery for urothelial carcinoma (UC) is a common clinical challenge, yet there is no established optimal treatment strategy to effectively control postoperative metastasis and recurrence. This case report evaluates the efficacy of total urethrectomy combined with adjuvant chemotherapy and PD-1 + antibody-drug conjugate (ADC) immunotherapy in managing UC urethral metastasis.

PATIENT CONCERNS

Three patients with a history of UC surgery presented with urethral metastasis recurrence, raising concerns about disease progression, treatment options, and long-term survival.

DIAGNOSES

All 3 patients were definitively diagnosed with UC urethral metastasis recurrence based on clinical, imaging, and histopathological examinations.

INTERVENTIONS

Each patient underwent total urethrectomy followed by adjuvant chemotherapy and PD-1 inhibitor + ADC combination immunotherapy.

OUTCOMES

Post-treatment follow-up, including serum tumor marker assessments and imaging studies, showed no significant recurrence. The patients exhibited prolonged overall survival and maintained a satisfactory postoperative quality of life.

LESSONS

Total urethrectomy combined with chemotherapy and PD-1+ADC immunotherapy may significantly improve outcomes in UC patients with postoperative urethral metastasis recurrence. This multimodal approach warrants further investigation in larger clinical studies.

Alleviation of Neurological Disorders by Targeting Neurodegenerative-Associated Enzymes: Natural and Synthetic Molecules

Neurological disorders, encompassing neurodegenerative and neuroinflammatory conditions, present significant public health and clinical challenges. Recent research has elucidated the pivotal role of various enzymes in the onset and progression of these disorders. This review explores the therapeutic potential of targeting these enzymes with natural and synthetic molecules. Key enzymes, including acetylcholinesterase, monoamine oxidase, beta-secretase, tau kinases, caspases, and cyclooxygenase-2, are implicated in diseases such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. Modulating these enzymes can alleviate symptoms, slow disease progression, or reverse pathological changes. Natural molecules derived from plants, microbes, seaweeds, and animals have long been noted for their therapeutic potential. Their ability to interact with specific enzymes with high specificity and minimal side effects makes them promising candidates for treatment. These natural agents provide a foundation for developing targeted therapies with improved safety profiles. Simultaneously, the development of synthetic chemistry has resulted in molecules designed to inhibit neurodegenerative enzymes with precision. This review examines the progress in creating small molecules, peptides, and enzyme inhibitors through sophisticated drug design techniques. It evaluates the efficacy, safety, and mechanisms of these synthetic agents, highlighting their potential for clinical application. The review offers a comprehensive overview of recent advancements in enzyme-targeted therapies for neurological disorders, covering both natural and synthetic molecules investigated in preclinical and clinical settings. It discusses the mechanisms through which these molecules exert their effects, the challenges faced in their development, and future research directions. By synthesizing current knowledge, this paper aims to illuminate the potential of enzyme-targeted interventions in managing neurological disorders, showcasing both the promise and limitations of these approaches.

Cardiotoxicity of small-molecule kinase inhibitors in cancer therapy

Cancer is one of the leading causes of death worldwide. Recent advances in precision oncology have enabled many specific cancer patient populations to respond well and achieve longer survival with small-molecule kinase inhibitors, which have become a new therapeutic strategy for tumors. Since 2001, the Food and Drug Administration has approved 108 and 63 new anticancer drugs for treating solid tumors and hematological malignancies, respectively, 89 of which belong to the large group of small-molecule kinase inhibitors (SMKIs). Compared to conventional chemotherapeutic agents such as cyclophosphamide, doxorubicin, and 5-FU, SMKIs offer better efficacy with fewer toxic side effects. Nevertheless, with the development of more novel SMKIs and their wider clinical application to a larger population of cancer patients, variable degrees of cardiotoxic adverse events have emerged for some SMKIs during cancer therapy. This review comprehensively summarizes the most updated progress in the cardiotoxicity of SMKIs in cancer therapy and discusses the new findings and mechanisms, which will provide emerging strategies for the prevention of cardiotoxicity caused by small molecule targeted drugs and the design of the next generation of low cardiotoxicity targeted drugs.

Proteolysis-Targeting Chimera (PROTAC): A Revolutionary Tool for Chemical Biology Research

Proteolysis-targeting chimera (PROTAC) technology is a revolutionary tool for drug discovery that simultaneously recruits E3 ligase and the protein of interest to induce ubiquitination and subsequent proteasomal degradation. Since the inaugural PROTAC prototype emerged in 2001, this modality has garnered significant interest across academia and industry, catalyzing transformative applications in drug discovery and chemical biology. The field has evolved from foundational investigations into molecular design, structural optimization, and protein target extension to address more sophisticated challenges, such as structural analysis of ternary complexes, expansion of diversified therapeutic indications, and clinical translation studies. Recent progress across chemical, pharmaceutical, and biochemical sciences has reshaped PROTAC design paradigms, which in turn expanded the chemical biology toolkit. In this review, pivotal milestones are systematically chronicled in PROTAC development, evaluate emerging strategies for diversifying E3 ligase utilization and expanding the scope of degradable targets, and summarize a series of instrumental and biochemical methodologies that propelled sequential breakthroughs. Additionally, forward-looking trajectories are proposed to address current limitations and accelerate the clinical maturation of PROTAC-based therapeutics.

Survival Outcomes in EGFR-Mutant Non-Small Cell Lung Cancer With Brain Metastases: Kaplan-Meier and Cox Regression Analyses Across Treatment Stages

BACKGROUND

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have shown significant efficacy in patients with brain metastases (BMs) from EGFR-mutated non-small cell lung cancer (NSCLC). However, acquired resistance is inevitable, and clinical data addressing key questions across treatment stages remain insufficient, limiting the formulation of precise treatment strategies.

METHODS

This retrospective study analyzed 302 EGFR-mutant NSCLC patients with BMs treated at Shandong Cancer Hospital (2014-2022). Patients were divided into three cohorts: cohort A (first-/second-generation EGFR-TKIs without third-generation use), cohort B (first-/second-generation followed by third-generation EGFR-TKIs), and cohort C (first-line third-generation EGFR-TKIs). Survival outcomes were evaluated using Kaplan-Meier and Cox regression analyses across three treatment stages. Propensity score matching (PSM) adjusted for baseline imbalances.

RESULTS

Third-generation EGFR-TKIs demonstrated superior progression-free survival (PFS) in first-line therapy compared to earlier-generation agents (median PFS1: 14.2 vs. 11.2 months; p = 0.0021), particularly for intracranial control (median iPFS1: 18.0 vs. 12.2 months; p = 0.0058). Patients with uncommon EGFR mutations had significantly shorter PFS on third-generation EGFR-TKIs than those with common mutations (4.4 vs. 12.9 months; p = 0.012). After resistance, combination therapy with immune checkpoint inhibitors (ICIs), antiangiogenics, and chemotherapy extended overall survival (OS) versus non-ICI regimens (median OS2: 17.3 vs. 10.4 months; p = 0.004).

CONCLUSIONS

Third-generation EGFR-TKIs are effective first-line options for BMs but show limited efficacy against uncommon mutations. Post-resistance regimens integrating ICIs, antiangiogenics, and chemotherapy may improve survival. Reassessment of genetic and PD-L1 status is critical for guiding sequential therapy.

Macrophage-derived exosomes in cancer: a double-edged sword with therapeutic potential

Solid cancer contains a complicated communication network between cancer cells and components in the tumor microenvironment (TME), significantly influencing the progression of cancer. Exosomes function as key carriers of signaling molecules in these communications, including the intricate signalings of tumor-associated macrophages (TAMs) on cancer cells and the TME. With their natural lipid bilayer structures and biological activity that relates to their original cell, exosomes have emerged as efficient carriers in studies on cancer therapy. Intrigued by the heterogeneity and plasticity of both macrophages and exosomes, we regard macrophage-derived exosomes in cancer as a double-edged sword. For instance, TAM-derived exosomes, educated by the TME, can promote resistance to cancer therapies, while macrophage-derived exosomes generated in vitro have shown favorable potential in cancer therapy. Here, we depict the reasons for the heterogeneity of TAM-derived exosomes, as well as the manifold roles of TAM-derived exosomes in cancer progression, metastasis, and resistance to cancer therapy. In particular, we emphasize the recent advancements of modified macrophage-derived exosomes in diverse cancer therapies, arguing that these modified exosomes are endowed with unique advantages by their macrophage origin. We outline the challenges in translating these scientific discoveries into clinical cancer therapy, aiming to provide patients with safe and effective treatments.

Targeted protein degradation in oncology: novel therapeutic opportunity for solid tumours?

Targeted and immune therapies have improved patient outcomes in selected diseases. Still, resistance inevitably occurs, and a significant portion of the proteome remains undruggable due to target localisation, structural or functional constraints. Targeted protein degraders (TPDs) represent a promising strategy to expand druggable targets by redirecting the ubiquitin-proteasome system to selectively degrade proteins of interest (POI). TPDs include proteolysis-targeting chimeras (PROTACs), which are heterobifunctional molecules that create a ternary complex with the POI and the E3 ligase, and molecular glues (MGs), which are monovalent small molecules that create an interface between an E3 ligase and the POI. Here, we provide a viewpoint on novel therapeutic opportunities offered by TPDs, notably through the targeting of previously undruggable proteins or overcoming some resistance mechanisms. We further present challenges that will need to be addressed in order to optimise clinical development, including dose optimisation, patient selection and drug delivery.

Identification of SURF4 and RALGAPA1 as promising therapeutic targets in glioblastoma and pan-cancer through integrative multi-omics, CRISPR-Cas9 screening and prognostic meta-analysis

Glioblastoma (GBM) is the most aggressive and malignant type of primary brain tumor, with a median survival time of less than two years and a uniformly poor prognosis, despite multimodal therapeutic approaches, which highlights an urgent need for novel therapeutic targets. In this study, by integrative multi-omics analysis from CPTAC database, DepMap database and seven independent GBM cohorts, four hub genes (CD44, SURF4, IGSF3 and RALGAPA1) were identified as essential genes regulated by cancer driver genes with robust prognostic value. GBM multi-omics data from public and in-house cohorts validated that CD44 and SURF4 might be synthetic lethal partners of loss-of-function tumor suppressor genes. Analysis for immune-related pathway activity revealed complex regulation relationships of the four hub genes in tumor microenvironment (TME). Further investigation on SURF4 in pathway activity, immune therapy response and drug sensitivity proposed that SURF4 emerged as a promising therapeutic target for GBM, even for pan-cancer. Pan-cancer multi-omics exploration suggested that RALGAPA1 may be a tumor suppressor gene. By screening the first-generation and second-generation DepMap database, four genes (CCDC106, GAL3ST1, GDI2 and HSF1) might be considered as synthetic targets after mutation of RALGAPA1 as a tumor suppressor gene.

HEX-1 reduces colitis-driven colorectal cancer via inactivating the prolyl isomerase PIN1 sensitization and remodeling the gut microbiota

Metabolic reprogramming, a pivotal hallmark of cancer, plays a crucial role in both the initiation and progression of colorectal cancer (CRC). Despite the vast unknowns surrounding the identity and biological activities of most natural metabolites in diseases, our study, utilizing native metabolomics results through GC-MS/MS, identified a small molecule, 4,4-Dimethyl-2-cyclohexen-1-one, named HEX-1 in the serum of CRC patients. We have further explored and assessed its biological activities. HEX-1 suppressed the proliferation of cancer cells and tumorigenesis via the inactivation and sensitization of PIN1. Notably, HEX-1 exhibits similar functional effects as all-trans retinoic acid (atRA) but stands out by not inducing the degradation of PIN1 mRNA or protein expression, unlike biological compounds associated with atRA. HEX-1 demonstrated the ability to induce G1/S arrest in vitro and ameliorate the progression of inflammatory CRC in mice by remodeling the gut microbiota. As volatile organic compounds (VOCs), HEX-1 could be detected feasibly. Its unique ability to penetrate whole cell populations positions it as a promising approach for cancer therapy and as an enhancer for chemotherapy and immunotherapy. The findings suggest that HEX-1 holds the potential as a valuable addition to the armamentarium against CRC.

Nanocarriers for cutting-edge cancer immunotherapies

Cancer immunotherapy aims to harness the body's own immune system for effective and long-lasting elimination of malignant neoplastic tissues. Owing to the advance in understanding of cancer pathology and immunology, many novel strategies for enhancing immunological responses against various cancers have been successfully developed, and some have translated into excellent clinical outcomes. As one promising strategy for the next generation of immunotherapies, activating the multi-cellular network (MCN) within the tumor microenvironment (TME) to deploy multiple mechanisms of action (MOAs) has attracted significant attention. To achieve this effectively and safely, delivering multiple or pleiotropic therapeutic cargoes to the targeted sites of cancerous tissues, cells, and intracellular organelles is critical, for which numerous nanocarriers have been developed and leveraged. In this review, we first introduce therapeutic payloads categorized according to their predicted functions in cancer immunotherapy and their physicochemical structures and forms. Then, various nanocarriers, along with their unique characteristics, properties, advantages, and limitations, are introduced with notable recent applications in cancer immunotherapy. Following discussions on targeting strategies, a summary of each nanocarrier matching with suitable therapeutic cargoes is provided with comprehensive background information for designing cancer immunotherapy regimens.

Exploring Novel Therapeutic Targets in Breast Cancer via Comprehensive Omics Profiling and Experimental Verification

BACKGROUND

Breast cancer is the leading cause of cancer-related deaths among women worldwide. Deciphering the molecular mechanisms of breast cancer is crucial for developing targeted therapeutic approaches.

METHODS

This study analyzed gene expression profiles from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) in breast cancer. Mendelian randomization (MR) analysis was then employed using publicly available eQTL databases to evaluate potential causal relationships between these DEGs and breast cancer. Enrichment analyses were further conducted to explore their functional significance. Furthermore, external validation of co-expressed genes was conducted using The Cancer Genome Atlas (TCGA) database. In vitro functional assays and drug sensitivity analyses were performed on selected target genes to validate their roles in breast cancer pathogenesis and treatment.

RESULTS

A total of 1052 upregulated and 1380 downregulated genes were identified in breast cancer. Additionally, MR analysis revealed 12 significant co-expressed genes potentially contributing to breast cancer pathogenesis. These genes were primarily enriched in lipid metabolism and immune responses via regulating microRNA functions and AMPK signaling. Validation through the TCGA database confirmed differential expression of these genes in breast cancer tissues. Strikingly, functional assays of the less-reported genes DNASE2 and ATOH8 demonstrated their involvement in breast cancer pathogenesis through modulating proliferation, migration, and invasion of cancer cells. Notably, several commonly used clinical drugs for breast cancer management, such as 5-Fluorouracil, exhibited dramatically increased sensitivity to DNASE2 and ATOH8 expression.

CONCLUSIONS

Our study provides novel insights into the molecular basis of breast cancer pathogenesis and identifies promising therapeutic strategies for this condition.

Medicinal Chemistry: A Key Driver in Achieving the Global Sustainable Development Goals

In 2015, the United Nations officially launched the Sustainable Development Goals (SDGs) as "the blueprint to achieve a better and more sustainable future for all. They address the global challenges we face, including those related to poverty, inequality, climate change, environmental degradation, peace and justice. The 17 Goals are all interconnected, in order to leave no one behind, it is important that we achieve them all by 2030". Here, we have embedded medicinal chemistry as a key player to achieve SDGs. We firmly believe that medicinal chemistry can and must contribute to a sustainable future and a better world with an improved quality of life for all. We have taken a critical look at each of the SDGs, dividing them into Priority and Foundational, and analyzed how medicinal chemistry has an impact on each of them. Although much has been done, we are determined to make progress in this area.

Mesothelin expression prediction in pancreatic cancer based on multimodal stochastic configuration networks

Predicting tumor biomarkers with high precision is essential for improving the diagnostic accuracy and developing more effective treatment strategies. This paper proposes a machine learning model that utilizes CT images and biopsy whole slide images (WSI) to classify mesothelin expression levels in pancreatic cancer. By combining multimodal learning and stochastic configuration networks, a radiopathomics mesothelin-prediction system named RPMSNet is developed. The system extracts radiomic and pathomic features from CT images and WSI, respectively, and sends them into stochastic configuration networks for the final prediction. Compared to traditional radiomics or pathomics, this system has the capability to capture more comprehensive image features, providing a multidimensional insight into tissue characteristics. The experiments and analyses demonstrate the accuracy and effectiveness of the system, with an area under the curve of 81.03%, an accuracy of 73.67%, a sensitivity of 71.54%, a precision of 76.78%, and a F1-score of 72.61%, surpassing both single-modality and dual-modality models. RPMSNet highlights its potential for early diagnosis and personalized treatment in precision medicine.

High-impact trials with genetic and -omics information focus on cancer mutations, are industry-funded, and less transparent

OBJECTIVES

To assess how genetics and -omics information is used in the most cited recent clinical trials and to evaluate industry involvement and transparency patterns.

STUDY DESIGN AND SETTING

This is a meta-research evaluation using a previously constructed database of the 600 most cited clinical trials published from 2019 to 2022. Trials that utilized genetic or -omics characterization of participants in the trial design, analysis, and results were considered eligible.

RESULTS

132 (22%) trials used genetic or -omics information, predominantly for detection of cancer mutations (n = 101). Utilization included eligibility criteria (n = 59), subgroup analysis (n = 82), and stratification factor in randomization (n = 14). Authors addressed the relevance in the conclusions in 82 studies (62%). 102 studies (77%) provided data availability statements and six had data already available. Most studies had industry funding (n = 111 [84.0%]). Oncology trials were more likely to be industry-funded (90.1% vs 64.5%, P = .001), to have industry-affiliated analysts (43.6% vs 22.6%, P = .036), and to favor industry-sponsored interventions (83.2% vs 58.1% P = .004). When compared to other trials, genetic and -omics trials were more likely to be funded by industry (84% vs 63.9%, P < .001) and tended to be less likely to have full protocols (P = .018) and statistical plans (P = .04) available.

CONCLUSION

Our study highlights the current underutilization of genetic and -omics technologies beyond testing for cancer mutations. Industry involvement in these trials appears to be more substantial and transparency is more limited, raising concerns about potential bias.

Dyr726, a brain-penetrant inhibitor of PI3Kα, Type III receptor tyrosine kinases, and WNT signaling

The vast majority of clinical small molecule multi-kinase inhibitors (mKI) report abject failures in targeting cancers with high stem cell contents like high-grade glioma and colorectal cancers. The FDA-approved mKIs to date ablate receptor tyrosine kinase signaling but do not target the paradoxical WNT signaling which is a key survival driver for the self-renewing cancer stem cells. The WNT pathway enhances cancer plasticity and triggers relapse of highly heterogenous tumours. Using de novo synthesis and structure-activity-relationship (SAR) studies with blood-brain-barrier (BBB) penetrant mKI scaffolds, we designed a highly potent and selective small molecule inhibitor of PI3Kα, PDGFR/KIT, and the WNT pathway denoted Dyr726. Dyr726 is superior to clinical mKIs and inhibits PI3K-AKT-mTOR and WNT-pathway signaling at multiple nodes thereby impeding proliferation, invasion, and tumour growth. Phospho-proteomic, structural, and target engagement analyses, combined with in vitro, in vivo efficacy, and pharmacokinetic studies reveal that Dyr726 is a brain-penetrant small molecule which effectively reduces tumour volume and extends survival of murine orthotopic models. Our current work establishes a first-in-class brain penetrant small molecule mKI which simultaneously antagonize the PI3K-AKT-mTOR and WNT pathways in preclinical cancer stem cell cultures, adult and pediatric primary organoids, and orthotopic murine models with positive efficacy in combination with clinical standard of care.

Validation of an LC-MS/MS Method for the Simultaneous Intracellular Quantification of the CDK4/6 Inhibitor Abemaciclib and the EZH2 Inhibitors GSK126 and Tazemetostat

Background: Inhibitors of cyclin-dependent kinases (CDKs) and epigenetic modifier enhancer of zeste homolog 2 (EZH2) have emerged as promising options in the pharmacotherapy of malignant tumors. Recently, we demonstrated synergistic antitumor effects of the CDK4/6 inhibitor abemaciclib and the EZH2 inhibitors GSK126 or tazemetostat in patient-derived glioblastoma (GBM) models. Importantly, all three drugs are substrates of the two most important plasma membrane multidrug transporters ABCB1 and ABCG2, with abemaciclib and tazemetostat also being inhibitors of these proteins. Methods: To investigate whether increased intracellular accumulation of either of the two drugs used in combination could have contributed to corresponding synergisms, we developed a simple LC-MS/MS method for simultaneous detection of the three substances in cell culture lysates. The method was validated in accordance with the current International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) guideline M10 on bioanalytical method validation and study sample analysis. Results: All acceptance criteria were met. Subsequent analysis of intracellular drug concentrations confirmed increased cellular uptake of tazemetostat in the presence of abemaciclib in both GBM cell lines studied compared to single agent treatment. A comparable pattern was also observed for GSK126, but in only one of the two cell lines used. Conclusions: In conclusion, the observed synergistic antitumor effect could be partly due to increased intracellular accumulation, although this alone is certainly not sufficient to explain it. Overall, the developed method provides a valuable approach for characterizing interactions at the transport level and for predicting the efficiency of both anticancer substance classes in different cell lines.

Chemoproteomic Profiling of PKA Substrates with Kinase-catalyzed Crosslinking and Immunoprecipitation (K-CLIP)

Phosphorylation is a highly regulated protein post-translational modification catalyzed by kinases. Kinases and phosphorylated proteins are key players in a myriad of cellular events, including cell signaling. When cell signaling networks are improperly regulated by kinases, various pathologies can arise, such as cancers and neurodegenerative disease. With critical roles in normal and disease biology, kinase-substrate interactions must be thoroughly characterized. Previously, the chemoproteomic method, kinase-catalyzed crosslinking and immunoprecipitation (K-CLIP), was developed to identify the kinases of a phosphoprotein substrate of interest. Here, K-CLIP was modified to profile the substrates of a kinase of interest. Specifically, the substrate profile of cAMP-dependent protein kinase (PKA) was studied with K-CLIP using a new ATP analog, ATP-alkyne aryl azide. Kinase-focused K-CLIP discovered SMC3 as a PKA substrate. With versatility for any kinase or phosphoprotein substrate of interest, K-CLIP will expand our understanding of kinase-mediated cell biology in healthy and diseased states.

Supramolecular Polymers for Drug Delivery

Supramolecular polymers are constructed through highly reversible and directionally specific non-covalent interactions between monomer units. This unique feature enables supramolecular polymers to undergo controlled structural reconfiguration and functional transformation in response to external stimuli, imparting them with high environmental responsiveness and self-healing properties. In particular, supramolecular polymers exhibit several specific advantages compared to conventional polymers, such as inherent degradability, the ease of preparation and the incorporation of functional units, and smart responsiveness to various biological stimuli. These characters make supramolecular polymers promising candidates for intelligent drug delivery systems in complex biological environments. In this review, we comprehensively summarize the latest developments and representative achievements of supramolecular polymers in drug delivery fields, focusing primarily on the design and synthesis, the properties and functionalities, and the practical applications of supramolecular polymers in small molecule drug delivery, gene therapy, and protein delivery. Finally, we highlight future research directions, focusing on multifunctionality, adaptability, and personalized therapy. We focus on recent studies that address key challenges in the field, providing rational polymer design, important properties, functionality, and understanding delivery strategies. These developments are expected to advance supramolecular polymers as new platforms of intelligent drug delivery systems, offering innovative solutions for the treatment of complex diseases.

Emergence of specific binding and catalysis from a designed generalist binding protein

The evolution of binding and catalysis played a central role in the emergence of life. While natural proteins have finely tuned affinities for their primary ligands, they also bind weakly and promiscuously to other molecules, which serve as starting points for stepwise, incremental evolution of entirely new specificities. Thus, modern proteins emerged from the joint exploration of sequence and structural space. The ability of natural proteins to bind promiscuously to small molecule fragments has been widely evaluated using methods including crystallographic fragment screening. However, this approach had not been applied to de novo proteins. Here, we apply this method to explore the promiscuity of a de novo small molecule-binding protein ABLE. As in Nature, we found ABLE was capable of forming weak complexes, which were found to be excellent starting points for evolving entirely new functions, including a binder of a turn-on fluorophore and a highly efficient and specific Kemp eliminase enzyme. This work shows how Nature and protein designers can take advantage of promiscuous binding interactions to evolve new proteins with specialized functions.

Xanthohumol Sensitizes Melanoma Cells to Vemurafenib by Lowering Membrane Cholesterol and Increasing Membrane Fluidity

Chemoresistance remains one of the major obstacles to cancer treatment. The search for specific molecules that could improve cancer treatment has become one of the objectives of biomedical research. Identifying new natural molecules to enhance chemotherapy treatment or improve sensitization to conventional therapies has become a key objective. Here, we evaluated the effect of Xanthohumol (XN) extracted from hop on SKMEL-28 melanoma cells and their sensitization to vemurafenib (VEM) treatment. We measured the XN effect on cell viability and apoptosis. We also assessed the effect of XN on membrane fluidity and membrane cholesterol levels. Finally, we studied the impact of XN on cell sensitization to VEM. Here, we showed that XN reduced SKMEL-28 cell viability through an apoptotic mechanism. Our results demonstrated the potential role of XN in sensitizing cancer cells to VEM with a less toxic effect on non-tumor cells. A study of XN's molecular mechanism showed that XN was able to induce cholesterol depletion and increased fluidity in SKMEL-28 cancer cells. This leads to an increase in VEM incorporation. Here, we describe the importance of the strategy to modulate membrane fluidity by XN in order to significantly improve anticancer therapy.

Decoding Drug Response With Structurized Gridding Map-Based Cell Representation

A thorough understanding of cell-line drug response mechanisms is crucial for drug development, repurposing, and resistance reversal. While targeted anticancer therapies have shown promise, not all cancers have well-established biomarkers to stratify drug response. Single-gene associations only explain a small fraction of the observed drug sensitivity, so a more comprehensive method is needed. However, while deep learning models have shown promise in predicting drug response in cell lines, they still face significant challenges when it comes to their application in clinical applications. Therefore, this study proposed a new strategy called DD-Response for cell-line drug response prediction. First, a limitation of narrow modeling horizons was overcome to expand the model training domain by integrating multiple datasets through source-specific label binarization. Second, a modified representation based on a two-dimensional structurized gridding map (SGM) was developed for cell lines & drugs, avoiding feature correlation neglect and potential information loss. Third, a dual-branch, multi-channel convolutional neural network-based model for pairwise response prediction was constructed, enabling accurate outcomes and improved exploration of underlying mechanisms. As a result, the DD-Response demonstrated superior performance, captured cell-line characteristic variations, and provided insights into key factors impacting cell-line drug response. In addition, DD-Response exhibited scalability in predicting clinical patient responses to drug therapy. Overall, because of DD-response's excellent ability to predict drug response and capture key molecules behind them, DD-response is expected to greatly facilitate drug discovery, repurposing, resistance reversal, and therapeutic optimization.

Tumor Metastasis: Mechanistic Insights and Therapeutic Intervention

Metastasis remains a leading cause of cancer‐related deaths, defined by a complex, multi‐step process in which tumor cells spread and form secondary growths in distant tissues. Despite substantial progress in understanding metastasis, the molecular mechanisms driving this process and the development of effective therapies remain incompletely understood. Elucidating the molecular pathways governing metastasis is essential for the discovery of innovative therapeutic targets. The rapid advancements in sequencing technologies and the expansion of biological databases have significantly deepened our understanding of the molecular drivers of metastasis and associated drug resistance. This review focuses on the molecular drivers of metastasis, particularly the roles of genetic mutations, epigenetic changes, and post‐translational modifications in metastasis progression. We also examine how the tumor microenvironment influences metastatic behavior and explore emerging therapeutic strategies, including targeted therapies and immunotherapies. Finally, we discuss future research directions, stressing the importance of novel treatment approaches and personalized strategies to overcome metastasis and improve patient outcomes. By integrating contemporary insights into the molecular basis of metastasis and therapeutic innovation, this review provides a comprehensive framework to guide future research and clinical advancements in metastatic cancer.

Identification of the therapeutic potential of novel TIGIT/PVR interaction blockers based advanced computational techniques and experimental validation

The inhibition of the TIGIT/PVR interaction demonstrates considerable anticancer properties by enhancing the cytotoxic activity of natural killer (NK) and CD8+ T cells. However, the development of small molecule inhibitors that target TIGIT is currently limited. In this study, small molecules with the capacity to bind TIGIT and block the TIGIT/PVR interaction were screened through an advanced computational process, subsequently confirmed by blocking assays. Combined machine learning model XGBOOST and centroid-based molecular docking were employed to expeditiously exclude negative molecules, thereby reducing the chemical space. Subsequently, a blockade assay targeting the TIGIT/PVR interaction was conducted on 14 candidate molecules along with positive control, wherein compound MCULE-5547257859 exhibited the most potent inhibitory effect. Molecular dynamics simulations and binding free energy analyses revealed that compound MCULE-5547257859 possesses a thermodynamically stable conformation, indicative of a stronger binding affinity to TIGIT. In conclusion, our investigation has delineated that compound MCULE-5547257859 effectively impedes the TIGIT/PVR interaction, thereby offering a novel therapeutic modality for oncology.

Drug screening approaches for small-molecule compounds in cancer-targeted therapy

Small-molecule compounds exhibit distinct pharmacological properties and clinical effectiveness. Over the past decade, advances in covalent drug discovery have led to successful small-molecule drugs, such as EGFR, BTK, and KRAS (G12C) inhibitors, for cancer therapy. Researchers are paying more attention to refining drug screening methods aiming for high throughput, fast speed, high specificity, and accuracy. Therefore, the discovery and development of small-molecule drugs has been facilitated by significantly reducing screening time and financial resources, and increasing promising lead compounds compared with traditional methods. This review aims to introduce classical and emerging methods for screening small-molecule compounds in targeted cancer therapy. It includes classification, principles, advantages, disadvantages, and successful applications, serving as valuable references for subsequent researchers.

Metal-organic framework-based smart stimuli-responsive drug delivery systems for cancer therapy: advances, challenges, and future perspectives

Cancer treatment is currently one of the most critical healthcare issues globally. A well-designed drug delivery system can precisely target tumor tissues, improve efficacy, and reduce damage to normal tissues. Stimuli-responsive drug delivery systems (SRDDSs) have shown promising application prospects. Intelligent nano drug delivery systems responsive to endogenous stimuli such as weak acidity, complex redox characteristics, hypoxia, active energy metabolism, as well as exogenous stimuli like high temperature, light, pressure, and magnetic fields are increasingly being applied in chemotherapy, radiotherapy, photothermal therapy, photodynamic therapy, and various other anticancer approaches. Metal-organic frameworks (MOFs) have become promising candidate materials for constructing SRDDSs due to their large surface area, tunable porosity and structure, ease of synthesis and modification, and good biocompatibility. This paper reviews the application of MOF-based SRDDSs in various modes of cancer therapy. It summarizes the key aspects, including the classification, synthesis, modifications, drug loading modes, stimuli-responsive mechanisms, and their roles in different cancer treatment modalities. Furthermore, we address the current challenges and summarize the potential applications of artificial intelligence in MOF synthesis. Finally, we propose strategies to enhance the efficacy and safety of MOF-based SRDDSs, ultimately aiming at facilitating their clinical translation.

Aspirin-responsive gene switch regulating therapeutic protein expression

Current small-molecule-regulated synthetic gene switches face clinical limitations such as cytotoxicity, long-term side-effects and metabolic disturbances. Here, we describe an advanced synthetic platform inducible by risk-free input medication (ASPIRIN), which is activated by acetylsalicylic acid (ASA/aspirin), a multifunctional drug with pain-relieving, anti-inflammatory, and cardiovascular benefits. To construct ASPIRIN, we repurpose plant salicylic acid receptors NPR1 and NPR4. Through domain truncations and high-throughput mutant library screening, we enhance their ASA sensitivity. Optimized NPR1 fused with a membrane-tethering myristoylation signal (Myr-NPR1) forms a complex with NPR4, which is fused with a DNA binding domain (VanR) and a transactivation domain (VP16). ASA induces dissociation of the Myr-NPR1/NPR4-VanR-VP16 complex, allowing nuclear translocation of NPR4-VanR-VP16 to activate VanR-operator-controlled gene expression. In male diabetic mice implanted with microencapsulated ASPIRIN-engineered cells, ASA regulates insulin expression, restores normoglycemia, alleviates pain and reduces biomarkers of diabetic neuropathy and inflammation. We envision this system will pave the way for aspirin-based combination gene therapies.

MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation

In hereditary papillary renal cell carcinoma (HPRCC), the hepatocyte growth factor receptor (MET) receptor tyrosine kinase (RTK) mutations recorded to date are located in the kinase domain and lead to constitutive MET activation. This contrasts with MET mutations identified in non-small cell lung cancer (NSCLC), which lead to exon 14 skipping and deletion of a regulatory domain: in this latter case, the mutated receptor still requires ligand stimulation. Sequencing of MET in samples from 158 HPRCC and 2808 NSCLC patients revealed ten uncharacterized mutations. Four of these, all found in HPRCC and leading to amino acid substitutions in the N-lobe of the MET kinase, proved able to induce cell transformation, which was further enhanced by hepatocyte growth factor (HGF) stimulation: His1086Leu, Ile1102Thr, Leu1130Ser and Cis1125Gly. Similar to the variant resulting in MET exon 14 skipping, the two N-lobe MET variants His1086Leu and Ile1102Thr were found to require stimulation by HGF in order to strongly activate downstream signaling pathways and epithelial cell motility. The Ile1102Thr mutation also displayed transforming potential, promoting tumor growth in a xenograft model. In addition, the N-lobe-mutated MET variants were found to trigger a common HGF-stimulation-dependent transcriptional program, consistent with an observed increase in cell motility and invasion. Altogether, this functional characterization revealed that N-lobe variants still require ligand stimulation, in contrast to other RTK variants. This suggests that HGF expression in the tumor microenvironment is important for tumor growth. The sensitivity of these variants to MET inhibitors opens the way for use of targeted therapies for patients harboring the corresponding mutations.

A first-in-class selective inhibitor of ERK1/2 and ERK5 overcomes drug resistance with a single-molecule strategy

Despite significant advancements in kinase-targeted therapy, the emergence of acquired drug resistance to targets such as KRAS and MEK remains a challenge. Extracellular-regulated kinase 1/2 (ERK1/2), positioned at the terminus of this pathway, is highly conserved and less susceptible to mutations, thereby garnering attention as a crucial therapeutical target. However, attempts to use monotherapies that target ERK1/2 have achieved only limited clinical success, mainly due to the issues of limited efficacy and the emergence of drug resistance. Herein, we present a proof of concept that extracellular-regulated kinase 5 (ERK5) acts as a compensatory pathway after ERK1/2 inhibition in triple-negative breast cancer (TNBC). By utilizing the principle of polypharmacology, we computationally designed SKLB-D18, a first-in-class molecule that selectively targets ERK1/2 and ERK5, with nanomolar potency and high specificity for both targets. SKLB-D18 demonstrated excellent tolerability in mice and demonstrated superior in vivo anti-tumor efficacy, not only exceeding the existing clinical ERK1/2 inhibitor BVD-523, but also the combination regimen of BVD-523 and the ERK5 inhibitor XMD8-92. Mechanistically, we showed that SKLB-D18, as an autophagy agonist, played a role in mammalian target of rapamycin (mTOR)/70 ribosomal protein S6 kinase (p70S6K) and nuclear receptor coactivator 4 (NCOA4)-mediated ferroptosis, which may mitigate multidrug resistance.

MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation

In hereditary papillary renal cell carcinoma (HPRCC), the hepatocyte growth factor receptor (MET) receptor tyrosine kinase (RTK) mutations recorded to date are located in the kinase domain and lead to constitutive MET activation. This contrasts with MET mutations identified in non-small-cell lung cancer (NSCLC), which lead to exon 14 skipping and deletion of a regulatory domain: In this latter case, the mutated receptor still requires ligand stimulation. Sequencing of MET in samples from 158 HPRCC and 2808 NSCLC patients revealed 10 uncharacterized mutations. Four of these, all found in HPRCC and leading to amino acid substitutions in the N-lobe of the MET kinase, proved able to induce cell transformation, which was further enhanced by hepatocyte growth factor (HGF) stimulation: His1086Leu, Ile1102Thr, Leu1130Ser, and Cis1125Gly. Similar to the variant resulting in MET exon 14 skipping, the two N-lobe MET variants His1086Leu and Ile1102Thr were found to require stimulation by HGF in order to strongly activate downstream signaling pathways and epithelial cell motility. The Ile1102Thr mutation also displayed transforming potential, promoting tumor growth in a xenograft model. In addition, the N-lobe-mutated MET variants were found to trigger a common HGF-stimulation-dependent transcriptional program, consistent with an observed increase in cell motility and invasion. Altogether, this functional characterization revealed that N-lobe variants still require ligand stimulation, in contrast to other RTK variants. This suggests that HGF expression in the tumor microenvironment is important for tumor growth. The sensitivity of these variants to MET inhibitors opens the way for use of targeted therapies for patients harboring the corresponding mutations.

Cancer vaccines: current status and future directions

Cancer continues to be a major global health burden, with high morbidity and mortality. Building on the success of immune checkpoint inhibitors and adoptive cellular therapy, cancer vaccines have garnered significant interest, but their clinical success remains modest. Benefiting from advancements in technology, many meticulously designed cancer vaccines have shown promise, warranting further investigations to reach their full potential. Cancer vaccines hold unique benefits, particularly for patients resistant to other therapies, and they offer the ability to initiate broad and durable T cell responses. In this review, we highlight the antigen selection for cancer vaccines, introduce the immune responses induced by vaccines, and propose strategies to enhance vaccine immunogenicity. Furthermore, we summarize key features and notable clinical advances of various vaccine platforms. Lastly, we delve into the mechanisms of tumor resistance and explore the potential benefits of combining cancer vaccines with standard treatments and other immunomodulatory approaches to improve vaccine efficacy.

New strategies to enhance the efficiency and precision of drug discovery

Drug discovery plays a crucial role in medicinal chemistry, serving as the cornerstone for developing new treatments to address a wide range of diseases. This review emphasizes the significance of advanced strategies, such as Click Chemistry, Targeted Protein Degradation (TPD), DNA-Encoded Libraries (DELs), and Computer-Aided Drug Design (CADD), in boosting the drug discovery process. Click Chemistry streamlines the synthesis of diverse compound libraries, facilitating efficient hit discovery and lead optimization. TPD harnesses natural degradation pathways to target previously undruggable proteins, while DELs enable high-throughput screening of millions of compounds. CADD employs computational methods to refine candidate selection and reduce resource expenditure. To demonstrate the utility of these methodologies, we highlight exemplary small molecules discovered in the past decade, along with a summary of marketed drugs and investigational new drugs that exemplify their clinical impact. These examples illustrate how these techniques directly contribute to advancing medicinal chemistry from the bench to bedside. Looking ahead, Artificial Intelligence (AI) technologies and interdisciplinary collaboration are poised to address the growing complexity of drug discovery. By fostering a deeper understanding of these transformative strategies, this review aims to inspire innovative research directions and further advance the field of medicinal chemistry.

Translational regulation of SND1 governs endothelial homeostasis during stress

Translational control shapes the proteome and is particularly important in regulating gene expression under stress. A key source of endothelial stress is treatment with tyrosine kinase inhibitors (TKIs), which lowers cancer mortality but increases cardiovascular mortality. Using a human induced pluripotent stem cell-derived endothelial cell (hiPSC-EC) model of sunitinib-induced vascular dysfunction combined with ribosome profiling, we assessed the role of translational control in hiPSC-ECs in response to stress. We identified staphylococcal nuclease and tudor domain-containing protein 1 (SND1) as a sunitinib-dependent translationally repressed gene. SND1 translational repression was mediated by the mTORC1/4E-BP1 pathway. SND1 inhibition led to endothelial dysfunction, whereas SND1 OE protected against sunitinib-induced endothelial dysfunction. Mechanistically, SND1 transcriptionally regulated UBE2N, an E2-conjugating enzyme that mediates K63-linked ubiquitination. UBE2N along with the E3 ligases RNF8 and RNF168 regulated the DNA damage repair response pathway to mitigate the deleterious effects of sunitinib. In silico analysis of FDA-approved drugs led to the identification of an ACE inhibitor, ramipril, that protected against sunitinib-induced vascular dysfunction in vitro and in vivo, all while preserving the efficacy of cancer therapy. Our study established a central role for translational control of SND1 in sunitinib-induced endothelial dysfunction that could potentially be therapeutically targeted to reduce sunitinib-induced vascular toxicity.

Tailoring cell-inspired biomaterials to fuel cancer therapy

Cancer stands as a predominant cause of mortality across the globe. Traditional cancer treatments, including surgery, radiotherapy, and chemotherapy, are effective yet face challenges like normal tissue damage, complications, and drug resistance. Biomaterials, with their advantages of high efficacy, targeting, and spatiotemporal controllability, have been widely used in cancer treatment. However, the biocompatibility limitations of traditional synthetic materials have restricted their clinical translation and application. Natural cell-inspired biomaterials inherently possess the targeting abilities of cells, biocompatibility, and immune evasion capabilities. Therefore, cell-inspired biomaterials can be used alone or in combination with other drugs or treatment strategies for cancer therapy. In this review, we first introduce the timeline of key milestones in cell-inspired biomaterials for cancer therapy. Then, we describe the abnormalities in cancer including biophysics, cellular biology, and molecular biology aspects. Afterwards, we summarize the design strategies of cell-inspired antitumor biomaterials. Subsequently, we elaborate on the application of antitumor biomaterials inspired by various cell types. Finally, we explore the current challenges and prospects of cell-inspired antitumor materials. This review aims to provide new opportunities and references for the development of antitumor cell-inspired biomaterials.

First-in-class ultralong-target-residence-time p38α inhibitors as a mitosis-targeted therapy for colorectal cancer

Colorectal cancer (CRC) constitutes the second leading cause of cancer-related death worldwide and advanced CRCs are resistant to targeted therapies, chemotherapies and immunotherapies. p38α (Mapk14) has been suggested as a therapeutic target in CRC; however, available p38α inhibitors only allow for insufficient target inhibition. Here we describe a unique class of p38α inhibitors with ultralong target residence times (designated ULTR-p38i) that robustly inhibit p38α downstream signaling and induce distinct biological phenotypes. ULTR-p38i monotherapy triggers an uncontrolled mitotic entry by activating Cdc25 and simultaneously blocking Wee1. Consequently, CRC cells undergo mitotic catastrophe, resulting in apoptosis or senescence. ULTR-p38i exhibit high selectivity, good pharmaco-kinetic properties and no measurable toxicity with strong therapeutic effects in patient-derived CRC organoids and syngeneic CRC mouse models. Conceptually, our study suggests ultralong-target-residence-time kinase inhibitors as an alternative to covalent inhibitors, which, because of the lack of cysteine residues, cannot be generated for many kinase cancer targets.

Precision Oncology in Clinical Practice: Two Years of Comprehensive Genomic Profiling in Croatia

Background: The widespread adoption of precision medicine in routine cancer care remains a critical challenge, even as advanced technologies expand and personalized therapies demonstrate remarkable success in certain cancer types. While breakthrough innovations in targeted treatments have revolutionized outcomes for specific cancers, translating these scientific advances into standard clinical practice continues to be an evolving and complex endeavor. Croatia has a nationwide project of precision oncology through the comprehensive genomic profiling (CGP) analysis. Since collecting and analyzing real-world data is crucial for clinical research and defining the value of CGP in precision oncology, we aimed to present the data from everyday clinical practice given the opportunities and challenges we faced. Methods: This was a retrospective observational study conducted at the national level in all patients whose tumor samples were subjected to CGP between 1 January 2020 and 31 December 2021. Results: In total, 481 patients with CGP results were included in this study. Gastrointestinal and reproductive malignancies were the most common, accounting for 29.1% and 28.9% of all tested tumors, respectively. Specifically, colorectal tumors made up 19.1% of cases, while uterine tumors represented 11.2%. At least one clinically relevant genomic alteration was found in 76.7% of patients, with the KRAS mutation (27.2%) being the most common. During the two-year study period, 26,709 individuals lost their lives to cancer in Croatia. Combining this with the CGP selection criteria valid at the time, there was an estimated population of approximately 13,350 potentially eligible patients for the CGP analysis, meaning that only 3.6% of potentially eligible patients were tested. Conclusions: The analysis identified clinically actionable genomic alterations in approximately 80% of the evaluated patients, suggesting they could be candidates for targeted therapeutic interventions. The adoption of CGP remains limited, with estimates indicating that under 5% of metastatic cancer patients received testing in the initial two-year implementation period, despite established national insurance coverage guidelines. This low utilization rate suggests a significant gap in access to genomic testing, leaving many eligible cancer patients without the potential benefits of this diagnostic approach.

LC-MS/MS method for quantification of 23 TKIs in Plasma: Assessing the relationship between anlotinib trough concentration and toxicities

OBJECTIVES

To develop a simple, rapid, and sensitive LC-MS/MS method for quantifying 23 tyrosine kinase inhibitors (TKIs) in plasma samples, and evaluate the relationship between the trough concentration of anlotinib(ANL) and its toxicities.

METHODS

The method was developed in Agilent 1290-6460 UHPLC-MS/MS system. This study prospectively enrolled 55 cancer patients undergoing ANL treatment. Plasma samples were collected at steady-state trough concentration and subsequently analyzed using the method. Patients were recorded for the occurrence of toxicities. Statistical analysis was performed to assess the association of the toxicities with ANL exposure level and patients' characteristics.

RESULTS

The LC-MS/MS method was developed and validated for all items required by pharmacopoeia. The results revealed a positive association between the trough concentration of ANL and the incidence of toxicities. The exposure level 17.655 ng/mL (AUC 0.82, p = 0.010) was identified as a predictive threshold value for grade ≥ 3 overall toxicities. In addition, lower platelet count (PLT count < 179 × 109 g/L) was significantly associated with higher occurrence of grade ≥ 3 toxicities (AUC 0.75, p = 0.049). A logistic model incorporating these two factors demonstrated improved diagnostic capacity for predicting ≥ 3 overall toxicities (AUC = 0.90, p = 0.001).

CONCLUSIONS

This study successfully developed and validated a simple, rapid, and sensitive LC-MS/MS method for quantifying 23 TKIs in plasma samples. Besides, this study found that both Ctrough of ANL and PLT count as independent predictors for ANL-induced ≥ 3 overall toxicities. Moreover, a logistic model including these two factors presents better prediction capacity for ≥ 3 overall toxicities.

Advances in the Repurposing and Blood-Brain Barrier Penetrance of Drugs in Pediatric Brain Tumors

Central nervous system (CNS) tumors are the leading cause of cancer-related mortality in children, with prognosis remaining dismal for some of these malignancies. Though the past two decades have seen advancements in surgery, radiation, and targeted therapy, major unresolved hurdles continue to undermine the therapeutic efficacy. These include challenges in suboptimal drug delivery through the blood-brain barrier (BBB), marked intra-tumoral molecular heterogeneity, and the elusive tumor microenvironment. Drug repurposing or re-tasking FDA-approved drugs with evidence of penetration into the CNS, using newer methods of intracranial drug delivery facilitating optimal drug exposure, has been an area of intense research. This could be a valuable tool, as most of these agents have already gone through the lengthy process of drug development and the evaluation of safety risks and the optimal pharmacokinetic profile. They can now be used and tested in clinics with an accelerated and different approach. Conclusions: The next-generation therapeutic strategy should prioritize repurposing oncologic and non-oncologic drugs that have been used for other indication, and have demonstrated robust preclinical activity against pediatric brain tumors. In combination with novel drug delivery techniques, these drugs could hold significant therapeutic promise in pediatric neurooncology.

Characterizing tumor biology and immune microenvironment in high-grade serous ovarian cancer via single-cell RNA sequencing: insights for targeted and personalized immunotherapy strategies

Background

High-grade serous ovarian cancer (HGSOC), the predominant subtype of epithelial ovarian cancer, is frequently diagnosed at an advanced stage due to its nonspecific early symptoms. Despite standard treatments, including cytoreductive surgery and platinum-based chemotherapy, significant improvements in survival have been limited. Understanding the molecular mechanisms, immune landscape, and drug sensitivity of HGSOC is crucial for developing more effective and personalized therapies. This study integrates insights from cancer immunology, molecular profiling, and drug sensitivity analysis to identify novel therapeutic targets and improve treatment outcomes. Utilizing single-cell RNA sequencing (scRNA-seq), the study systematically examines tumor heterogeneity and immune microenvironment, focusing on biomarkers influencing drug response and immune activity, aiming to enhance patient outcomes and quality of life.

Methods

scRNA-seq data was obtained from the GEO database in this study. Differential gene expression was analyzed using gene ontology and gene set enrichment methods. InferCNV identified malignant epithelial cells, while Monocle, Cytotrace, and Slingshot software inferred subtype differentiation trajectories. The CellChat software package predicted cellular communication between malignant cell subtypes and other cells, while pySCENIC analysis was utilized to identify transcription factor regulatory networks within malignant cell subtypes. Finally, the analysis results were validated through functional experiments, and a prognostic model was developed to assess prognosis, immune infiltration, and drug sensitivity across various risk groups.

Results

This study investigated the cellular heterogeneity of HGSOC using scRNA-seq, focusing on tumor cell subtypes and their interactions within the tumor microenvironment. We confirmed the key role of the C2 IGF2+ tumor cell subtype in HGSOC, which was significantly associated with poor prognosis and high levels of chromosomal copy number variations. This subtype was located at the terminal differentiation of the tumor, displaying a higher degree of malignancy and close association with stage IIIC tissue types. The C2 subtype was also associated with various metabolic pathways, such as glycolysis and riboflavin metabolism, as well as programmed cell death processes. The study highlighted the complex interactions between the C2 subtype and fibroblasts through the MK signaling pathway, which may be closely related to tumor-associated fibroblasts and tumor progression. Elevated expression of PRRX1 was significantly connected to the C2 subtype and may impact disease progression by modulating gene transcription. A prognostic model based on the C2 subtype demonstrated its association with adverse prognosis outcomes, emphasizing the importance of immune infiltration and drug sensitivity analysis in clinical intervention strategies.

Conclusion

This study integrates molecular oncology, immunotherapy, and drug sensitivity analysis to reveal the mechanisms driving HGSOC progression and treatment resistance. The C2 IGF2+ tumor subtype, linked to poor prognosis, offers a promising target for future therapies. Emphasizing immune infiltration and drug sensitivity, the research highlights personalized strategies to improve survival and quality of life for HGSOC patients.

AMG 193, a Clinical Stage MTA-Cooperative PRMT5 Inhibitor, Drives Antitumor Activity Preclinically and in Patients with MTAP-Deleted Cancers

One of the most robust synthetic lethal interactions observed in multiple functional genomic screens has been the dependency on protein arginine methyltransferase 5 (PRMT5) in cancer cells with MTAP deletion. We report the discovery of the clinical stage MTA-cooperative PRMT5 inhibitor AMG 193, which preferentially binds PRMT5 in the presence of MTA and has potent biochemical and cellular activity in MTAP-deleted cells across multiple cancer lineages. In vitro, PRMT5 inhibition induces DNA damage, cell cycle arrest, and aberrant alternative mRNA splicing in MTAP-deleted cells. In human cell line and patient-derived xenograft models, AMG 193 induces robust antitumor activity and is well tolerated with no impact on normal hematopoietic cell lineages. AMG 193 synergizes with chemotherapies or the KRAS G12C inhibitor sotorasib in vitro and combination treatment in vivo substantially inhibits tumor growth. AMG 193 is demonstrating promising clinical activity, including confirmed partial responses in patients with MTAP-deleted solid tumors from an ongoing phase 1/2 study. Significance: AMG 193 preferentially inhibits the growth of MTAP-deleted tumor cells by inhibiting PRMT5 when in complex with MTA, thus sparing MTAP wild-type normal cells. AMG 193 shows promise as a targeted therapy in a clinically defined patient population.

Acquired resistance to tyrosine kinase targeted therapy: mechanism and tackling strategies

Over the past two decades, tyrosine kinase inhibitors (TKIs) have rapidly emerged as pivotal targeted agents, offering promising therapeutic prospects for patients. However, as the cornerstone of targeted therapies, an increasing number of TKIs have been found to develop acquired resistance during treatment, making the challenge of overcoming this resistance a primary focus of current research. This review comprehensively examines the evolution of TKIs from multiple perspectives, with particular emphasis on the mechanisms underlying acquired resistance, innovative drug design strategies, inherent challenges, and future directions.

SUZ12-Increased NRF2 Alleviates Cardiac Ischemia/Reperfusion Injury by Regulating Apoptosis, Inflammation, and Ferroptosis

Nuclear factor erythroid 2-related factor 2 (NRF2) is a redox-sensitive transcriptional factor that enables cells to resist oxidant responses, ferroptosis and inflammation. Here, we set out to probe the effects of NRF2 on cardiomyocyte injury under acute myocardial infarction (AMI) condition and its potential mechanism. Human cardiomyocytes were exposed to hypoxia/reoxygenation (H/R) to induce cell injury. qRT-PCR and western blot assays were used to detect the levels of mRNAs and proteins. Cardiomyocyte injury was determined by detecting the levels of lactate dehydrogenase and creatine Kinase MB (CK-MB). Cell apoptosis was investigated by flow cytometry and related markers. Levels of IL-6, IL-10, and TNF-α were measured by ELISA. Cell ferroptosis was assessed by detecting the production of reactive oxygen species (ROS), malonaldehyde (MDA), reduced glutathione/oxidized glutathione disulfide (GSH/GSSG) ratio, Fe + content, and related regulators. The interaction between NRF2 and the suppressor of zest 12 (SUZ12) was analyzed by using dual-luciferase reporter and RNA immunoprecipitation assays. AMI rat models were established for in vivo analysis. NRF2 was lowly expressed in AMI patients and H/R-induced cardiomyocytes. Forced expression of NRF2 reduced H/R-induced cardiomyocyte injury, apoptosis, inflammation, and ferroptosis. Moreover, NRF2 overexpression improved cardiac function and injury in vivo. Mechanistically, SUZ12 bound to the promoter of NRF2 and promoted its expression. Further functional analyses showed that SUZ12 overexpression reduced H/R-induced cardiomyocyte injury, apoptosis, inflammation, and ferroptosis, which were reversed by NRF2 silencing. SUZ12-increased NRF2 suppressed H/R-induced cardiomyocyte injury, apoptosis, inflammation, and ferroptosis in vitro and improved cardiac functions in rats with I/R injury, suggesting the potential cardioprotective effect of NRF2 in cardiac injury during AMI.

The role of DDR1 in cancer and the progress of its selective inhibitors

Discoidin domain receptor 1 (DDR1) is a member of the receptor tyrosine kinase superfamily, which mainly activates downstream signaling pathways through binding to collagen. The abnormal expression of DDR1 is closely related to the occurrence and development of various tumors, and it is one of the potential targets for molecular targeted therapy. At present, specific antibodies and selective small molecule inhibitors against DDR1 have been approved for Phase I clinical trials. In this review, we summarized the effects of DDR1 on tumor cell proliferation, survival, migration, invasion, energy metabolism and tumor microenvironment, and combed the research progress of selective DDR1 small molecule inhibitors in the field of anti-tumor. It is hoped that more DDR1 inhibitors with excellent performance will be developed to provide more treatment options for tumor patients.