Small molecules targeting protein-protein interactions for cancer therapy

Optimization of antimicrobial peptide Smp43 as novel inhibitors of Cancer

Smp43 is a natural antimicrobial peptide derived from scorpion venom containing 43 amino acids, which inhibits the proliferation of various cancer cells, providing a new surrogate for antitumor drug discovery. However, Smp43 is large (Mw: 4653 Da) and unstable as a linear peptide. We truncated Smp43 to identify the key fragment and found that Smp(1-14) displayed significant antitumor activity. Subsequent optimization of Smp(1-14) led to a series of stapled peptides, among which SSmp6 demonstrated enhanced antitumor activity, stability, and membrane permeability compared to the linear peptides. Moreover, SSmp6 could decrease the phosphorylation of AKT, damage cancer cell membranes, and induce cell apoptosis. The results highlight the potential of SSmp6 as a lead stapled peptide for developing novel antitumor therapies. The study introduces a concept for using antimicrobial peptides to develop anticancer drugs.

Computer-Aided Drug Discovery for Undruggable Targets

Undruggable targets are those of therapeutical significance but challenging for conventional drug design approaches. Such targets often exhibit unique features, including highly dynamic structures, a lack of well-defined ligand-binding pockets, the presence of highly conserved active sites, and functional modulation by protein-protein interactions. Recent advances in computational simulations and artificial intelligence have revolutionized the drug design landscape, giving rise to innovative strategies for overcoming these obstacles. In this review, we highlight the latest progress in computational approaches for drug design against undruggable targets, present several successful case studies, and discuss remaining challenges and future directions. Special emphasis is placed on four primary target categories: intrinsically disordered proteins, protein allosteric regulation, protein-protein interactions, and protein degradation, along with discussion of emerging target types. We also examine how AI-driven methodologies have transformed the field, from applications in protein-ligand complex structure prediction and virtual screening to de novo ligand generation for undruggable targets. Integration of computational methods with experimental techniques is expected to bring further breakthroughs to overcome the hurdles of undruggable targets. As the field continues to evolve, these advancements hold great promise to expand the druggable space, offering new therapeutic opportunities for previously untreatable diseases.

Design, synthesis, and biological evaluation of novel and highly potent peptides targeting syntenin

Syntenin, an intracellular scaffold protein, plays a critical role in renal cell carcinoma (RCC) progression, underscoring its potential as a therapeutic target. Herein, we report a novel, highly efficient, and stable peptide inhibitor (PDPP-3) that exhibits excellent inhibitory effects on syntenin. We have constructed a combined virtual screening scheme based on pharmacophore modeling and molecular docking to identify six potential d-amino acid-containing peptide inhibitors targeting syntenin. Among them, PDPP-3 showed the best inhibitory activity against syntenin. Binding affinity experiments and biostability experiments indicated that the interaction between PDPP-3 and syntenin displayed nanomolar-level binding affinity (Kd = 6.15 ± 0.12 nM) and superior biostability in serum. Molecular dynamics simulation results further confirmed that PDPP-3 could stably bind to the active site of syntenin. Additionally, cytotoxicity test results showed that PDPP-3 exhibited potent inhibitory effects on various types of renal cancer cells, with the best inhibitory effect on SK-RC-20 cells. More importantly, PDPP-3 significantly downregulates the expression of matrix metalloenzymes MT1-MMP and MMP2, which are pivotal for tumor invasion, and demonstrates inhibitory effects on tumor growth in SK-RC-20 derived xenografts. These data suggest that PDPP-3 may be a very promising candidate drug for the treatment of RCC.

The value of coimmunoprecipitation (Co-IP) assays in drug discovery

INTRODUCTION

Co-IP assays are well-established technologies widely applicated for investigating the mechanisms underlying protein-protein interactions and identifying protein-protein interaction modulators. These assays play an important role in elucidating the complex networks of protein interactions critical for cellular functions.

AREAS COVERED

This review covers a technical protocol of standard Co-IP. The research contents and conclusions of Co-IP in protein-protein interactions and protein-protein interaction modulators are summarized. Finally, three derivations of Co-IP assays are introduced. Literature was surveyed from original publications, standard sources, PubMed and clinical trials through 14 April 2025.

EXPERT OPINION

To perform Co-IP successfully, researchers must consider the selection of specific antibody, remission of nonspecific binding and detection limitations for transient or weak interactions. Co-IP assays offer several advantages over tandem affinity purification and pull-down methods, particularly in their applicability to primary cells. This allows for the study of PPIs in a natural cellular environment. Conventional Co-IP assays often struggle to detect weak or transient interactions and can suffer from nonspecific binding contamination. However, advancements in Co-IP techniques address these challenges, enhancing sensitivity and specificity, and enabling the detection of subtle interactions while distinguishing specific binding events. This makes Co-IP a powerful tool for exploring the dynamics of protein interactions in living systems.

Injectable polydopamine/curcumin dual-modified polylactic acid/polycaprolactone coaxial staple fibers for chronotropic treatment of oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most prevalent malignant tumors in the oral and maxillofacial region. Traditional treatments for OSCC, including surgery, radiotherapy, and chemotherapy, often lead to severe adverse effects. Therefore, the development of safe and effective novel cancer therapies is crucial for achieving synergistic cancer treatment, significantly enhancing patient survival and quality of life. In this study, triaxial electrospinning combined with freeze-shortening technology was employed to prepare injectable short fibers that provided a sustained release of curcumin (CUR). Subsequently, polydopamine (PDA) was modified on the surface of the short fibers to create PDA@CUR@PCL/PLA. The developed injectable short fibers represented a significant advancement in reducing the risks associated with the surgical implantation of traditional two-dimensional fibrous membranes. These fibers were coated with dopamine, which imparted notable significant photothermal effects, facilitating the rapid destruction of cancer cells. Furthermore, the core-loaded CUR was released in a pH-responsive manner and demonstrated a sustained anti-tumor effect. Cellular and animal experiments indicated that these composite short fibers could effectively eliminate oral cancer cells through a synergistic combination of photothermal and drug therapies without apparent toxic side effects. The developed injectable coaxial PDA@CUR@PCL/PLA short fibers are expected to provide a novel treatment approach for OSCC.

Salicylaldehyde Benzoylhydrazones with Anticancer Activity and Selectivity: Design, Synthesis, and In Vitro Evaluation

Dimethoxy derivatives of salicylaldehyde benzoylhydrazone containing a methoxy group on both aromatic rings were designed and synthesized. The compounds were obtained in high yields, and their structures were confirmed by elemental analysis and various spectral techniques. In vitro evaluation of dimethoxy hydrazones demonstrated potent activity against the leukemic cell lines at low micro- and nanomolar concentrations. Remarkably, two dimethoxy analogs showed exceptional antileukemic selectivity, with no toxicity observed in normal human embryonic kidney HEK-293 cells. In silico modeling identified likely interactions with the target, human cAbl kinase, and suggested a possible mechanism for their antileukemic activity.

Innovative design and potential applications of covalent strategy in drug discovery

Covalent inhibitors provide persistent inhibition while maintaining excellent selectivity and efficacy by creating stable covalent connections with specific amino acids in target proteins. This technique enables the precise inhibition of previously undruggable targets, lowering the frequency of administration and potentially bypassing drug resistance. Because of these advantages, covalent inhibitors have tremendous potential in treating cancer, inflammation, and infectious illnesses, making them extremely important in modern pharmacological research. Covalent inhibitors targeting EGFR, BTK, and KRAS (G12X), which overcome drug resistance and off-target, non-"medicinal" difficulties, as well as covalent inhibitors targeting SARS-CoV-2 Mpro, have paved the way for the development of new antiviral medicines. Furthermore, the use of covalent methods in drug discovery procedures, such as covalent PROTACs, covalent molecular gels, covalent probes, CoLDR, and Dual-targeted covalent inhibitors, preserves these tactics' inherent features while incorporating the advantages of covalent inhibitors. This synthesis opens up new therapeutic opportunities. This review comprehensively examines the use of covalent techniques in drug discovery, emphasizing their transformational potential for future drug development.

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.

Exploring the landscape of post-translational modification in drug discovery

Post-translational modifications (PTMs) play a crucial role in regulating protein function, and their dysregulation is frequently associated with various diseases. The emergence of epigenetic drugs targeting factors such as histone deacetylases (HDACs) and histone methyltransferase enhancers of zeste homolog 2 (EZH2) has led to a significant shift towards precision medicine, offering new possibilities to overcome the limitations of traditional therapeutics. In this review, we aim to systematically explore how small molecules modulate PTMs. We discuss the direct targeting of enzymes involved in PTM pathways, the modulation of substrate proteins, and the disruption of protein-enzyme interactions that govern PTM processes. Additionally, we delve into the emerging strategy of employing multifunctional molecules to precisely regulate the modification levels of proteins of interest (POIs). Furthermore, we examine the specific characteristics of these molecules, evaluating their therapeutic benefits and potential drawbacks. The goal of this review is to provide a comprehensive understanding of PTM-targeting strategies and their potential for personalized medicine, offering a forward-looking perspective on the evolution of precision therapeutics.

DeepTGIN: a novel hybrid multimodal approach using transformers and graph isomorphism networks for protein-ligand binding affinity prediction

Predicting protein-ligand binding affinity is essential for understanding protein-ligand interactions and advancing drug discovery. Recent research has demonstrated the advantages of sequence-based models and graph-based models. In this study, we present a novel hybrid multimodal approach, DeepTGIN, which integrates transformers and graph isomorphism networks to predict protein-ligand binding affinity. DeepTGIN is designed to learn sequence and graph features efficiently. The DeepTGIN model comprises three modules: the data representation module, the encoder module, and the prediction module. The transformer encoder learns sequential features from proteins and protein pockets separately, while the graph isomorphism network extracts graph features from the ligands. To evaluate the performance of DeepTGIN, we compared it with state-of-the-art models using the PDBbind 2016 core set and PDBbind 2013 core set. DeepTGIN outperforms these models in terms of R, RMSE, MAE, SD, and CI metrics. Ablation studies further demonstrate the effectiveness of the ligand features and the encoder module. The code is available at: https://github.com/zhc-moushang/DeepTGIN . SCIENTIFIC CONTRIBUTION: DeepTGIN is a novel hybrid multimodal deep learning model for predict protein-ligand binding affinity. The model combines the Transformer encoder to extract sequence features from protein and protein pocket, while integrating graph isomorphism networks to capture features from the ligand. This model addresses the limitations of existing methods in exploring protein pocket and ligand features.

Pesticide-induced metabolic disruptions in crops: A global perspective at the molecular level

Pesticide pollution has emerged as a critical global environmental issue of pervasive concern. Although the application of pesticides has provided substantial benefits in controlling weeds, pests, and crop diseases, their indiscriminate use poses considerable challenges to soil health and food safety. Pesticides can be absorbed by crops through either foliar or root uptake, resulting in deleterious effects such as extensive tissue damage, growth inhibition, and reduced crop quality. Beside these visible effects, pesticides can alter gene expression and disrupt cellular signaling transduction, thereby interfering with essential metabolic processes even inducing toxic stress. Moreover, pesticides can interact intricately with biomolecules (e.g. proteins, nucleic acid) in crops, causing significant alterations in protein structure and physiological function. This review focuses on pesticide residues and their associated toxicity, emphasizing their pervasive influence on vital physiological and metabolic pathways, including carbohydrate metabolism, amino acid metabolism, and fatty acid metabolism. Particular attention is given to elucidating the molecular mechanisms underlying these disturbances, specifically regarding transcriptional regulation, cell signaling pathways, and biomolecular interactions. This review provides a comprehensive understanding of multifaceted effects of pesticides and to underscore the necessity for sustainable agricultural practices to safeguard crop yield and quality.

Discovering new mode-of-action pesticide leads inhibiting protein-protein interactions: example targeting plant O-acetylserine sulfhydrylase

BACKGROUND

The widespread evolution of pesticide resistance poses a significant challenge to current agriculture, necessitating the discovery of molecules with new modes of action. Despite extensive efforts, no major molecules with new modes of action have been commercialized for decades. Most pesticides function by binding to specific pockets on target enzymes, enabling a single target site mutation to confer resistance. An alternative approach is the disruption of protein-protein interactions (PPI), which require complementary mutations on both interacting partners for resistance to occur. Thus, our aim is the discovery and design of small-molecule inhibitors that target the interface of the PPI complex of O-acetylserine sulfhydrylase (OASS) and serine acetyltransferase (SAT), key obligatory interacting plant enzymes involved in the biosynthesis of the amino acid cysteine.

RESULTS

By employing in silico filtering techniques on a virtual library of 30 million small molecules, we identified initial hits capable of binding OASS and interfering with its interaction with a peptide derived from SAT with a half-maximal inhibitory concentration (IC50) of 34 μm. Subsequently, we conducted molecular chemical optimizations, generating an early lead molecule (PJ4) with an IC50 value of 4 μm. PJ4 successfully inhibited the germination of Arabidopsis thaliana seedlings and inhibited clover growth in a pre-emergence application at an effective concentration of 4.6 kg ha-1.

CONCLUSION

These new compounds described herein can serve as promising leads for further optimization as herbicides with a new mode-of-action. This technology can be used for discovering new modes of action chemicals inhibiting all pest groups. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Design, synthesis, and evaluation of dual son of sevenless 1 (SOS1) and epidermal growth factor receptor (EGFR) inhibitors for the treatment of cancers

The treatment of KRAS mutant tumors remains challenging and dual-targeted small-molecule drugs are considered to be innovative therapeutic alternatives. Herein, we discovered a series of SOS1 and EGFR dual inhibitors by employing a fused pharmacophore strategy and structural optimization. Notably, compound 4 exhibited potent SOS1 (IC50 = 8.3 nM) and EGFR (IC50 = 14.6 nM) inhibitory activities and markedly inhibited the proliferation of other KRAS-mutant cancer cell lines. Furthermore, Western blot analysis confirmed that compound 4 effectively reduced the level of downstream p-ERK. These results indicated that compound 4 could serve as a potential compound for treating KRAS mutant tumors.

An update on small molecule compounds targeting synthetic lethality for cancer therapy

Targeting cancer-specific vulnerabilities through synthetic lethality (SL) is an emerging paradigm in precision oncology. A SL strategy based on PARP inhibitors has demonstrated clinical efficacy. Advances in DNA damage response (DDR) uncover novel SL gene pairs. Beyond BRCA-PARP, emerging SL targets like ATR, ATM, DNA-PK, CHK1, WEE1, CDK12, RAD51, and RAD52 show clinical promise. Selective and bioavailable small molecule inhibitors have been developed to induce SL, but optimization for potency, specificity, and drug-like properties remains challenging. This article illuminated recent progress in the field of medicinal chemistry centered on the rational design of agents capable of eliciting SL specifically in neoplastic cells. It is envisioned that innovative strategies harnessing SL for small molecule design may unlock novel prospects for targeted cancer therapeutics going forward.

Discovery and mechanistic insights into thieno[3,2-d]pyrimidine and heterocyclic fused pyrimidines inhibitors targeting tubulin for cancer therapy

Guided by the X-ray cocrystal structure of the lead compound 4a, we developed a series of thieno[3,2-d]pyrimidine and heterocyclic fused pyrimidines demonstrating potent antiproliferative activity against four tumor cell lines. Two analogs, 13 and 25d, exhibited IC50 values around 1 nM and overcame P-glycoprotein (P-gp)-mediated multidrug resistance (MDR). At low concentrations, 13 and 25d inhibited both the colony formation of SKOV3 cells in vitro and tubulin polymerization. Furthermore, mechanistic studies showed that 13 and 25d induced G2/M phase arrest and apoptosis in SKOV3 cells, as well as dose-dependent inhibition of tumor cell migration and invasion at low concentrations. Most notably, the X-ray cocrystal structures of compounds 4a, 25a, and the optimal molecule 13 in complex with tubulin were elucidated. This study identifies thieno[3,2-d]pyrimidine and heterocyclic fused pyrimidines as representatives of colchicine-binding site inhibitors (CBSIs) with potent antiproliferative activity.

Targeting HSP90 for Cancer Therapy: Current Progress and Emerging Prospects

Heat shock protein 90 (HSP90), a highly conserved member of the heat shock protein family, regulates various proteins and signaling pathways involved in cancer, making it a promising target for cancer therapy. Traditional HSP90 inhibitors have demonstrated significant antitumor potential in preclinical trials, with over 20 compounds advancing to clinical trials and showing promising results. However, the limited clinical efficacy and shared toxicity of these inhibitors restrict their further clinical use. Encouragingly, developing novel inhibitors using conventional medicinal chemistry approaches─such as selective inhibitors, dual inhibitors, protein-protein interaction inhibitors, and proteolysis-targeting chimeras─is expected to address these challenges. Notably, the selective inhibitor TAS-116 has already been successfully marketed. In this Perspective, we summarize the structure, biological functions, and roles of HSP90 in cancer, analyze the clinical status of HSP90 inhibitors, and highlight the latest advancements in novel strategies, offering insights into their future development.

Small Molecular Inhibitors That Target ATM for Drug Discovery: Current Research and Potential Prospective

The protein kinase ataxia telangiectasia mutated (ATM) is a constituent of the phosphatidylinositol 3-kinase-related kinase (PIKK) family, exerting a pivotal influence on diverse cellular processes, notably the signaling of double-strand DNA breaks (DSB) and stress response. The dysregulation of ATM is implicated in the pathogenesis of cancer and other diseases such as neurodegeneration. Hence, ATM is deemed a promising candidate for potential therapeutic interventions across a spectrum of diseases. Presently, while ATM small molecule inhibitors are not commercially available, various selective inhibitors have progressed to the clinical research phase. Specifically, AZD1390, WSD0628, SYH2051, and ZN-B-2262 are under investigation in clinical studies pertaining to glioblastoma multiforme and advanced solid tumors, respectively. In this Perspective, we encapsulate the structure, biological functions, and disease relevance of ATM. Subsequently, we concentrate on the design concepts and structure-activity relationships (SAR) of ATM inhibitors, delineating potential avenues for the development of more efficacious ATM-targeted inhibitors.

Development and therapeutic perspectives of CXCR4 antagonists for disease therapy

Chemokine receptor 4 (CXCR4) is a subtype receptor protein of the GPCR family with a seven-transmembrane structure widely distributed in human tissues. CXCR4 is involved in diseases (e.g., HIV-1 infection), cancer proliferation and metastasis, inflammation signaling pathways, and leukemia, making it a promising drug target. Clinical trials on CXCR4 antagonists mainly focused on peptides and antibodies, with a few small molecule compounds, such as AMD11070 (2) and MSX-122 (3), showing promise in cancer treatment. This perspective discusses the structure-activity relationship (SAR) of CXCR4 and its role in diseases, mainly focusing on the SAR of CXCR4 antagonists. It also explores the standard structural features and target interactions of CXCR4 binding in different disease categories. Furthermore, it investigates various modification strategies to propose potential improvements in the effectiveness of CXCR4 drugs.

Beyond ribosomal function: RPS6 deficiency suppresses cholangiocarcinoma cell growth by disrupting alternative splicing

Cholangiocarcinoma (CCA) is a bile duct malignancy with a dismal prognosis. This study systematically investigated the role of the ribosomal protein S6 (RPS6) gene, which is dependent in CCA. We found that RPS6 upregulation in CCA tissues was correlated with a poor prognosis. Functional investigations have shown that alterations in RPS6 expression, both gain- and loss-of function could affect the proliferation of CCA cells. In xenograft tumor models, RPS6 overexpression enhances tumorigenicity, whereas RPS6 silencing reduces it. Integration analysis using RNA-seq and proteomics elucidated downstream signaling pathways of RPS6 depletion by affecting the cell cycle, especially DNA replication. Immunoprecipitation followed by mass spectrometry has identified numerous spliceosome complex proteins associated with RPS6. Transcriptomic profiling revealed that RPS6 affects numerous alternative splicing (AS) events, and combined with RNA immunoprecipitation sequencing, revealed that minichromosome maintenance complex component 7 (MCM7) binds to RPS6, which regulates its AS and increases oncogenic activity in CCA. Targeting RPS6 with vivo phosphorodiamidate morpholino oligomer (V-PMO) significantly inhibited the growth of CCA cells, patient-derived organoids, and subcutaneous xenograft tumor. Taken together, the data demonstrate that RPS6 is an oncogenic regulator in CCA and that RPS6-V-PMO could be repositioned as a promising strategy for treating CCA.

Recent advances in Alzheimer's disease: Mechanisms, clinical trials and new drug development strategies

Alzheimer's disease (AD) stands as the predominant form of dementia, presenting significant and escalating global challenges. Its etiology is intricate and diverse, stemming from a combination of factors such as aging, genetics, and environment. Our current understanding of AD pathologies involves various hypotheses, such as the cholinergic, amyloid, tau protein, inflammatory, oxidative stress, metal ion, glutamate excitotoxicity, microbiota-gut-brain axis, and abnormal autophagy. Nonetheless, unraveling the interplay among these pathological aspects and pinpointing the primary initiators of AD require further elucidation and validation. In the past decades, most clinical drugs have been discontinued due to limited effectiveness or adverse effects. Presently, available drugs primarily offer symptomatic relief and often accompanied by undesirable side effects. However, recent approvals of aducanumab (1) and lecanemab (2) by the Food and Drug Administration (FDA) present the potential in disrease-modifying effects. Nevertheless, the long-term efficacy and safety of these drugs need further validation. Consequently, the quest for safer and more effective AD drugs persists as a formidable and pressing task. This review discusses the current understanding of AD pathogenesis, advances in diagnostic biomarkers, the latest updates of clinical trials, and emerging technologies for AD drug development. We highlight recent progress in the discovery of selective inhibitors, dual-target inhibitors, allosteric modulators, covalent inhibitors, proteolysis-targeting chimeras (PROTACs), and protein-protein interaction (PPI) modulators. Our goal is to provide insights into the prospective development and clinical application of novel AD drugs.

Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy

The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.

Finding the partner: FRET and beyond

Given the importance of aberrant protein-protein interactions (PPIs) in disease, the recent drug discovery focuses on targeting the altered PPIs to treat the disease. In this context, identifying the atypical PPIs underlying the disease is critical for the development of diagnostics and therapeutics. Various biochemical, biophysical, and genetic methods have been reported to study PPIs. Here, we are giving a short account of those techniques with more emphasis on Förster resonance energy transfer (FRET), which can be used to monitor macromolecular interactions in live cells. Besides the basics of FRET, we explain the modifications of its application, like Single molecule FRET (smFRET), Fluorescence Lifetime Imaging Microscopy-FRET (FLIM-FRET), and photoswitching FRET. While smFRET is extensively used for evaluating the biology of nucleic acids and also to develop diagnostics, FLIM-FRET is widely exploited to study the PPIs underlying neurological disorders and cancer. Photoswitching FRET is a relatively newer technique and it has tremendous potential to unravel the significance of different PPIs. Besides these modifications, there are several advancements in the field by introducing new fluorophores. Identification of lanthanide chelates, quantum dots, and other nanoparticle fluorophores has revolutionized the applications of FRET in diagnostics and basic biology. Yet, these methods can be employed to study the interactions of only two molecules. Since the majority of the PPIs are multimeric complexes, we still need to improve our technologies to study these interactions in live cells in real-time.

MGPPI: multiscale graph neural networks for explainable protein-protein interaction prediction

Protein-Protein Interactions (PPIs) involves in various biological processes, which are of significant importance in cancer diagnosis and drug development. Computational based PPI prediction methods are more preferred due to their low cost and high accuracy. However, existing protein structure based methods are insufficient in the extraction of protein structural information. Furthermore, most methods are less interpretable, which hinder their practical application in the biomedical field. In this paper, we propose MGPPI, which is a Multiscale graph convolutional neural network model for PPI prediction. By incorporating multiscale module into the Graph Neural Network (GNN) and constructing multi convolutional layers, MGPPI can effectively capture both local and global protein structure information. For model interpretability, we introduce a novel visual explanation method named Gradient Weighted interaction Activation Mapping (Grad-WAM), which can highlight key binding residue sites. We evaluate the performance of MGPPI by comparing with state-of-the-arts methods on various datasets. Results shows that MGPPI outperforms other methods significantly and exhibits strong generalization capabilities on the multi-species dataset. As a practical case study, we predicted the binding affinity between the spike (S) protein of SARS-COV-2 and the human ACE2 receptor protein, and successfully identified key binding sites with known binding functions. Key binding sites mutation in PPIs can affect cancer patient survival statues. Therefore, we further verified Grad-WAM highlighted residue sites in separating patients survival groups in several different cancer type datasets. According to our results, some of the highlighted residues can be used as biomarkers in predicting patients survival probability. All these results together demonstrate the high accuracy and practical application value of MGPPI. Our method not only addresses the limitations of existing approaches but also can assists researchers in identifying crucial drug targets and help guide personalized cancer treatment.

Directly targeting BAX for drug discovery: Therapeutic opportunities and challenges

For over two decades, the development of B-cell lymphoma-2 (Bcl-2) family therapeutics has primarily focused on anti-apoptotic proteins, resulting in the first-in-class drugs called BH3 mimetics, especially for Bcl-2 inhibitor Venetoclax. The pro-apoptotic protein Bcl-2-associated X protein (BAX) plays a crucial role as the executioner protein of the mitochondrial regulated cell death, contributing to organismal development, tissue homeostasis, and immunity. The dysregulation of BAX is closely associated with the onset and progression of diseases characterized by pathologic cell survival or death, such as cancer, neurodegeneration, and heart failure. In addition to conducting thorough investigations into the physiological modulation of BAX, research on the regulatory mechanisms of small molecules identified through biochemical screening approaches has prompted the identification of functional and potentially druggable binding sites on BAX, as well as diverse all-molecule BAX modulators. This review presents recent advancements in elucidating the physiological and pharmacological modulation of BAX and in identifying potentially druggable binding sites on BAX. Furthermore, it highlights the structural and mechanistic insights into small-molecule modulators targeting diverse binding surfaces or conformations of BAX, offering a promising avenue for developing next-generation apoptosis modulators to treat a wide range of diseases associated with dysregulated cell death by directly targeting BAX.

Sesamolin serves as an MYH14 inhibitor to sensitize endometrial cancer to chemotherapy and endocrine therapy via suppressing MYH9/GSK3β/β-catenin signaling

BACKGROUND

Endometrial cancer (EC) is one of the most common gynecological cancers. Herein, we aimed to define the role of specific myosin family members in EC because this protein family is involved in the progression of various cancers.

METHODS

Bioinformatics analyses were performed to reveal EC patients' prognosis-associated genes in patients with EC. Furthermore, colony formation, immunofluorescence, cell counting kit 8, wound healing, and transwell assays as well as coimmunoprecipitation, cycloheximide chase, luciferase reporter, and cellular thermal shift assays were performed to functionally and mechanistically analyze human EC samples, cell lines, and a mouse model, respectively.

RESULTS

Machine learning techniques identified MYH14, a member of the myosin family, as the prognosis-associated gene in patients with EC. Furthermore, bioinformatics analyses based on public databases showed that MYH14 was associated with EC chemoresistance. Moreover, immunohistochemistry validated MYH14 upregulation in EC cases compared with that in normal controls and confirmed that MYH14 was an independent and unfavorable prognostic indicator of EC. MYH14 impaired cell sensitivity to carboplatin, paclitaxel, and progesterone, and increased cell proliferation and metastasis in EC. The mechanistic study showed that MYH14 interacted with MYH9 and impaired GSK3β-mediated β-catenin ubiquitination and degradation, thus facilitating the Wnt/β-catenin signaling pathway and epithelial-mesenchymal transition. Sesamolin, a natural compound extracted from Sesamum indicum (L.), directly targeted MYH14 and attenuated EC progression. Additionally, the compound disrupted the interplay between MYH14 and MYH9 and repressed MYH9-regulated Wnt/β-catenin signaling. The in vivo study further verified sesamolin as a therapeutic drug without side effects.

CONCLUSIONS

Herein, we identified that EC prognosis-associated MYH14 was independently responsible for poor overall survival time of patients, and it augmented EC progression by activating Wnt/β-catenin signaling. Targeting MYH14 by sesamolin, a cytotoxicity-based approach, can be applied synergistically with chemotherapy and endocrine therapy to eventually mitigate EC development. This study emphasizes MYH14 as a potential target and sesamolin as a valuable natural drug for EC therapy.

Phase separation of Nur77 mediates XS561-induced apoptosis by promoting the formation of Nur77/Bcl-2 condensates

The orphan nuclear receptor Nur77 is a critical regulator of the survival and death of tumor cells. The pro-death effect of Nur77 can be regulated by its interaction with Bcl-2, resulting in conversion of Bcl-2 from a survival to killer. As Bcl-2 is overexpressed in various cancers preventing them from apoptosis and promoting their resistance to chemotherapy, targeting the apoptotic pathway of Nur77/Bcl-2 may lead to new cancer therapeutics. Here, we report our identification of XS561 as a novel Nur77 ligand that induces apoptosis of tumor cells by activating the Nur77/Bcl-2 pathway. In vitro and animal studies revealed an apoptotic effect of XS561 in a range of tumor cell lines including MDA-MB-231 triple-negative breast cancer (TNBC) and MCF-7/LCC2 tamoxifen-resistant breast cancer (TAMR) in a Nur77-dependent manner. Mechanistic studies showed XS561 potently induced the translocation of Nur77 from the nucleus to mitochondria, resulting in mitochondria-related apoptosis. Interestingly, XS561-induced accumulation of Nur77 at mitochondria was associated with XS561 induction of Nur77 phase separation and the formation of Nur77/Bcl-2 condensates. Together, our studies identify XS561 as a new activator of the Nur77/Bcl-2 apoptotic pathway and reveal a role of phase separation in mediating the apoptotic effect of Nur77 at mitochondria.

Evolution of chemistry and selection technology for DNA-encoded library

DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.

Targeting autophagy and beyond: Deconvoluting the complexity of Beclin-1 from biological function to cancer therapy

Beclin-1 is the firstly-identified mammalian protein of the autophagy machinery, which functions as a molecular scaffold for the assembly of PI3KC3 (class III phosphatidylinositol 3 kinase) complex, thus controlling autophagy induction and other cellular trafficking events. Notably, there is mounting evidence establishing the implications of Beclin-1 in diverse tumorigenesis processes, including tumor suppression and progression as well as resistance to cancer therapeutics and CSC (cancer stem-like cell) maintenance. More importantly, Beclin-1 has been confirmed as a potential target for the treatment of multiple cancers. In this review, we provide a comprehensive survey of the structure, functions, and regulations of Beclin-1, and we discuss recent advances in understanding the controversial roles of Beclin-1 in oncology. Moreover, we focus on summarizing the targeted Beclin-1-regulating strategies in cancer therapy, providing novel insights into a promising strategy for regulating Beclin-1 to improve cancer therapeutics in the future.

The permissive binding theory of cancer

The later stages of cancer, including the invasion and colonization of new tissues, are actively mysterious compared to earlier stages like primary tumor formation. While we lack many details about both, we do have an apparently successful explanatory framework for the earlier stages: one in which genetic mutations hold ultimate causal and explanatory power. By contrast, on both empirical and conceptual grounds, it is not currently clear that mutations alone can explain the later stages of cancer. Can a different type of molecular change do better? Here, I introduce the "permissive binding theory" of cancer, which proposes that novel protein binding interactions are the key causal and explanatory entity in invasion and metastasis. It posits that binding is more abundant at baseline than we observe because it is restricted in normal physiology; that any large perturbation to physiological state revives this baseline abundance, unleashing many new binding interactions; and that a subset of these cause the cellular functions at the heart of oncogenesis, especially invasion and metastasis. Significant physiological perturbations occur in cancer cells in very early stages, and generally become more extreme with progression, providing interactions that continually fuel invasion and metastasis. The theory is compatible with, but not limited to, causal roles for the diverse molecular changes observed in cancer (e.g. gene expression or epigenetic changes), as these generally act causally upstream of proteins, and so may exert their effects by changing the protein binding interactions that occur in the cell. This admits the possibility that molecular changes that appear quite different may actually converge in creating the same few protein complexes, simplifying our picture of invasion and metastasis. If correct, the theory offers a concrete therapeutic strategy: targeting the key novel complexes. The theory is straightforwardly testable by large-scale identification of protein interactions in different cancers.