Search Results (174)

Brain-derived neurotrophic factor (BDNF) is a key mediator of central sensitization and chronic pain through activation of TrkB receptors. Although the Pannexin 1 (Panx1) channel has been implicated in chronic pain, its involvement in BDNF-TrkB signaling remains unclear. Here, we investigated the functional relationship between TrkB activation and Panx1 using a BDNF-induced pain model in rats. Animals received a single intrathecal administration of BDNF, and mechanical nociception was assessed using the Randall–Selitto test. Behavioral analyses were combined with pharmacological interventions, Western blotting, confocal microscopy, YOPRO-1 uptake assays, and ATP quantification in spinal cord tissue. Intrathecal BDNF induced a robust mechanical hyperalgesia that persisted for up to 10 days. Blockade of Panx1 with 10Panx significantly attenuated BDNF-induced hyperalgesia. BDNF increased Src416 phosphorylation, Panx1 phosphorylation, and YOPRO-1 uptake in dorsal horn neurons, indicating enhanced channel activation. These effects were prevented by the TrkB antagonist ANA12, demonstrating that Panx1 acts downstream of BDNF-TrkB signaling. Inhibition of Src-family kinases with PP2 reduced both hyperalgesia and Panx1 activation, supporting a TrkB-Src-Panx1 signaling cascade. Furthermore, BDNF enhanced ATP release from spinal cord slices, an effect abolished by ANA12, PP2, and 10Panx. Together, these findings identify Panx1 as a downstream effector engaged by BDNF-TrkB signaling during the onset of mechanical hyperalgesia. While persistent TrkB activation appears to be required for the prolonged nociceptive state, the Src family kinase-Panx1 pathway contributes primarily to the early phase of BDNF-induced sensitization. Full article

Mitochondria coordinate cellular energy production, metabolism, and signalling through the organization of the electron transport chain (ETC) and formation of respiratory supercomplexes. These structures facilitate efficient electron transfer and enable coenzyme Q (CoQ) channelling, allowing differential regulation of NADH- and succinate-driven respiration while modulating reactive oxygen species (ROS) production. Beyond their damaging potential, ROS act as key signalling molecules that regulate mitochondrial function through redox-sensitive modifications. Mitochondrial protein kinases add an additional layer of control, with Src-family kinases playing a central role. In particular, the mitochondrial tyrosine-kinase Fgr is activated by H₂O₂ and promotes phosphorylation of succinate dehydrogenase, boosting complex II activity, delivering more electrons to CoQ and inducing reverse electron transfer (RET) through CI, in a ROS-induced ROS generation amplification cycle. This induces a metabolic rewiring aimed at supporting stress adaptation, immune cell activation, and macrophage polarization. Overall, the interplay between supercomplex organization, ROS signalling, and kinase activity is critical for metabolic flexibility and represents a promising target for therapeutic intervention. Full article

CD36 is a multifunctional scavenger receptor involved in long-chain fatty acid (LCFA) uptake, binding of oxidized lipids, and interactions with extracellular matrix proteins such as thrombospondin-1. Through association with Src family kinases, integrins, and adaptor proteins, it also modulates signaling, migration, inflammation, angiogenesis, and phagocytosis. Hypoxia, a common feature of solid tumors, inflamed tissues, and ischemic organs, remodels CD36 expression, localization, and function through hypoxia-inducible factor (HIF) signaling and stress-activated kinases. These effects change cellular metabolism, intercellular lipid trafficking, and cell behavior (migration, phagocytosis, angiogenesis, immune phenotype) in a manner that is highly dependent on tissue type, duration of hypoxia, and metabolic context, with important implications for disease progression. In acute hypoxia, CD36 regulation often contributes to rapid metabolic adaptation, whereas in chronic hypoxia, it may promote sustained lipid accumulation, inflammation, maladaptive remodeling, or tumor progression. In this review, we aim to highlight the regulation and function of CD36 in hypoxia in different tissues, conditions, and metabolic states, emphasizing the distinct roles of CD36 in acute versus chronic hypoxia and its potential therapeutic implications. For example, hypoxia typically downregulates CD36 in ischemic cardiomyocytes to limit lipotoxic fatty acid influx, whereas in hepatocytes, adipocytes, and tumor-associated macrophages, it upregulates CD36-mediated lipid uptake to sustain steatotic, inflammatory, or protumorigenic metabolism, illustrating the tissue-specific nature of this regulation. Full article

Sickle cell disease (SCD) is an autosomal recessive hemoglobin disorder that is mainly characterized by the presence of hemoglobin S (HbS; point mutation [Glu6Val] in the beta-globin gene). Under deoxygenated conditions, HbS polymerizes and serves as the primary trigger of oxidative stress in red blood cells (RBCs), promoting polymerization of Band 3, a major membrane scaffold protein that links the lipid bilayer to the spectrin–ankyrin cytoskeletal network. Phosphorylation at key residues within the cytosolic domain of Band 3 induces conformational changes that weaken ankyrin binding and enhance lateral mobility and clustering of Band 3. These effects are mediated through a coordinated network of erythrocyte tyrosine kinases, primarily spleen tyrosine kinase (SYK) and sarcoma (Src) family kinases, which act sequentially to modify distinct tyrosine residues. Structural features of these kinases, including tandem SH2 domains in SYK and conserved SH2–SH3–kinase domain architecture of Src family members, enable precise recognition of phosphotyrosine motifs and propagation of phosphorylation cascades. Sequence alignment and structural superimposition of SH2 domains across studied kinases demonstrate a highly conserved fold that is critical for phosphotyrosine recognition, suggesting potential overlap in substrate engagement. Therapeutically, targeting these kinases has shown considerable promise, as tyrosine kinase inhibitors (TKIs) reduce Band 3 phosphorylation, restore RBC deformability, and decrease hemolysis and vaso-occlusive interactions in vitro. Thus, in this narrative review, we focus on the regulation of Band 3 by the above-mentioned tyrosine kinases, as well as the therapeutic potential of TKIs in SCD. Full article

Allergic rhinitis (AR) is one of the most prevalent allergic disorders worldwide. Current pharmacological treatments are often limited by suboptimal efficacy and notable adverse effects. Herbal medicines, with their multi-component and multi-target therapeutic characteristics, have attracted increasing attention. Artemisia ordosica Krasch. (AOK), a traditional Chinese/Mongolian medicine has demonstrated immunomodulatory, antioxidant, and anti-inflammatory activities. The anti-AR potential of AOK extract fractions was evaluated using in vitro mast cell degranulation inhibition assays, network pharmacology analysis, molecular docking, and molecular dynamics simulations to elucidate underlying pharmacological mechanisms. The P815 mast cell model induced by compound 48/80 was employed to assess the inhibitory activity and cytotoxicity of different extract fractions. Among the tested fractions, the ethyl acetate fraction exhibited the most potent inhibitory effect on mast cell degranulation without significant cytotoxicity. Network pharmacology analysis identified 254 potential AR-related targets of AOK, with Signal Transducer and Activator of Transcription 3(STAT3), Src protein(SRC), Tumor protein 53(TP53), AKT Serine/Threonine Kinase 1(AKT1), Heat Shock Protein 90 Alpha Family Class A Member 1(HSP90AA1), Estrogen Receptor 1(ESR1), and Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha(PIK3CA) identified as key hub proteins. Gene Ontology and KEGG pathway enrichment analyses indicated that AOK primarily modulated inflammatory and oxidative stress-related processes through the lipid and atherosclerosis, hypoxia-inducible factor-1, and AGE-RAGE signaling pathways. Molecular docking and dynamics simulations demonstrated strong binding affinities and stable interactions between major active constituents, particularly hydroxygenkwanin, and key targets such as SRC. The ethyl acetate fraction of AOK extract exhibited significant mast cell degranulation inhibitory activity, likely mediated via a synergistic multi-component, multi-target mechanism involving regulation of inflammatory and immune-related signaling pathways. These findings provide a pharmacological basis for the potential application of AOK in AR treatment. Full article

Background: Cytokine-induced JAK–STAT signaling becomes dysregulated in chronic human diseases, including cancer and autoimmunity, and contributes to immune cell dysfunction. A cytokine-independent approach to activating STAT proteins could “hardwire” pro-survival and effector programs in immune cells to sustain function within diseased tissues. Engineered variants of the herpesvirus saimiri tyrosine kinase interacting protein (TIP) can recruit the SRC family kinase (SFK) LCK to drive STAT phosphorylation and activation. Here, we evaluated the interactome of a TIP-derived, cytokine-independent STAT5 activator and determined whether it could induce STAT5 activation in immune cell lines and primary human CD8+ T cells. Methods: A STAT5 activator (aSTAT5) was characterized by proteomics using affinity purification mass spectrometry (AP-MS) to define its interactome and STAT5 binding specificity. STAT5 phosphorylation was assessed in hematopoietic cell lines and primary human CD8+ T cells. Results: Proteomic analysis confirmed preferential association of aSTAT5 with STAT5 relative to other proteins. In cell-based assays, aSTAT5 induced robust STAT5 phosphorylation in LCK-expressing NK-92 and Jurkat T cells, whereas phosphorylation was not observed in Raji B cells or RAW 264.7 macrophages despite expression of closely related SFKs and STAT5. Cytokine-independent STAT5 phosphorylation supported the viability of NK-92 cells and primary human CD8+ T cells during cytokine withdrawal and preserved the cytotoxic function of CAR T cells. Conclusions: We defined the interactome of a cytokine-independent STAT5 activator and demonstrated its capacity to maintain survival and function in human CD8+ T cells and NK-92 cells. These findings underscore the translational potential of engineered, cytokine-independent STAT5 activation for immune cell therapies. Full article

Background: The coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, remains a significant threat to global health. This continued threat is due to the emergence of new variants, the immune system’s limited ability to respond, and the limited effectiveness of available treatments for all individuals. Therefore, leveraging drug repurposing, a fast and inexpensive way to find other drugs that have already been shown to be safe and efficacious, becomes useful. This study leverages ADMET profiling, network pharmacology, and molecular docking to evaluate the repurposing of Product Nkabinde for COVID-19 treatment. Methods: ADMET analysis involving the bioactive phytochemicals of PN was evaluated for pharmacokinetic appropriateness and drug-likeness. Using topological analysis, a network of protein–protein interactions was built to identify hub genes, and predicted compound targets were intersected with COVID-19-associated genes to find shared targets. Their biological importance was characterized using functional enrichment analysis. The binding affinities of PN phytochemicals against hub proteins and SARS-CoV-2 viral proteases (Mpro and PLpro) were assessed by molecular docking using AutoDock Vina. To confirm docking accuracy, co-crystallized ligands were redocked using Schrodinger 2022-1. The multi-target therapeutic potential of PN in COVID-19 was assessed using this integrative network pharmacology and molecular docking technique. Results: Molecular docking demonstrated that PN phytochemicals displayed robust and persistent binding affinities for both viral and host targets. Oleanolic acid showed the best affinity toward Mpro (−12.9 kcal/mol vs. −8.3 kcal/mol), while quercetin-3-O-β-D-(6′-galloyl)-glucopyranoside showed better binding to PLpro (−8.4 kcal/mol vs. −6.4 kcal/mol). Procyanidin B2 toward HCK (−10.5 vs. −7.9 kcal/mol), diosgenin toward EGFR (−9.4 vs. −8.4 kcal/mol), rutin toward SRC (−10.5 vs. −7.8 kcal/mol), and pimelea factor P2 toward PIK3R1 (−11.0 vs. −8.2 kcal/mol) all showed significantly higher affinities than their corresponding co-crystallized ligands. Furthermore, procyanidin B2 demonstrated consistent binding to STAT1 and STAT3, confirming its role in modulating immune signals. Most of the PN phytochemicals show advantageous pharmacokinetic properties, including elevated anticipated gastrointestinal absorption and adherence to Lipinski’s rule of five, signifying favorable oral bioavailability and drug-like properties. Moreover, PN exhibits a remarkable multi-target binding capacity against both SARS-CoV-2 proteases and key host signaling proteins involved in immune regulation and inflammatory responses, as determined by this integrative network pharmacology and molecular docking investigation. Conclusions: PN’s prospects as a host-directed, antiviral treatment for COVID-19 are demonstrated by its coordinated modulation of the PI3K/AKT, JAK–STAT, SRC-family kinase, EGFR, and SYK pathways. These results necessitate further experimental and clinical validation, providing a solid computational basis for repurposing PN in the treatment of COVID-19. Full article

Chondroitin sulfate (CS) chains are major components of the extra- and pericellular matrix in the central nervous system (CNS), and their sulfation patterns influence CNS development and function. Highly sulfated CS preparations, including CS-D- and CS-E-enriched forms, have been shown to facilitate neurite outgrowth in cultured mouse hippocampal neurons. Notably, neurons cultured on CS-D- or CS-E-enriched substrates exhibited the following distinct morphological characteristics: CS-D promoted the extension of multiple short neurites, whereas CS-E induced the formation of a single elongated neurite with a polarization-like morphology. These features are consistent with early stages of neuronal polarization. However, the specific roles of these highly sulfated CS forms in polarization-like morphology remain unclear. In this study, we demonstrate that polarization-like morphological transitions in hippocampal neurons can be modulated on mixed CS-D/CS-E substrates by varying their ratios. Compared with CS-D-enriched substrates, CS-E-enriched substrates more effectively promoted polarization-like neuronal morphology, accompanied by enhanced activation of Src-family kinases. Furthermore, forced activation of Fyn kinase induced morphological changes resembling polarization-like features in a neuroblastoma cell line, even in the absence of CS-D/CS-E mixed substrates. In conclusion, highly sulfated CS subtypes may function as extracellular cues that regulate neuronal morphology via Src-family signaling, with likely involvement of Fyn. Full article

Background: YES1 is an Src family non-receptor tyrosine-protein kinase that regulates cell growth, migration, survival, and oncogenic signaling. Although YES1 activation mechanisms and substrates have been extensively studied, its phosphosite-specific regulation across diverse biological contexts remains poorly understood. Methods: We performed a large-scale integrative analysis of 3825 publicly available human mass spectrometry-based phosphoproteomic datasets to map YES1 phosphorylation events. Co-modulation, co-occurrence, evolutionary conservation, and disease-association analyses were conducted to characterize the functional and clinical relevance of site-specific YES1 phosphorylation. Results: Y426 emerged as the predominant YES1 phosphosite across diverse biological conditions, localized within the activation loop of the kinase domain and conserved across Src family kinases. Co-modulation analysis identified 421 positively and 102 negatively associated phosphosites enriched in biological processes related to cell cycle regulation, transcription, cytoskeletal remodeling, apoptosis, and carcinogenesis. Among these high-confidence protein phosphosites, we identified 24 binary interactors, 5 upstream regulators, and 8 candidate downstream substrates. Comparison with DisGeNet cancer biomarkers showed overlap between YES1-associated phosphoproteomic signatures and site-specific oncogenic markers across multiple cancers, such as breast cancer, colorectal cancer, leukemia, and lung adenocarcinoma. Conclusions: This study provides a systems-level, phosphosite-focused view of YES1 signaling and supports a central regulatory role for Y426 within global phosphoregulatory and cancer-associated networks. Full article

Background: Hepatitis B virus (HBV) infection continues to be a major public health concern, especially in sub-Saharan Africa, where widespread epidemics and restricted availability of long-term antiviral therapies result in higher mortality and morbidity rates. Drug repurposing represents a strategic approach to accelerate the discovery of effective therapies by leveraging agents with demonstrated antiviral and immunomodulatory activity. Product Nkabinde (PN) is a patented African polyherbal formulation initially developed for the treatment of HIV. Recent experimental studies demonstrate PN’s potent anti-HIV activity and significant immunomodulatory effects in human immune cells, implicating host-directed mechanisms relevant to chronic viral infections. This study combines an integrative application of network pharmacology and molecular docking to evaluate the repurposing potential of PN as a multi-target agent in HBV. Method: Bioactive components of PN were screened, and compound-associated targets were intersected with HBV-associated genes (proteins) to construct a protein–protein interaction (PPI) network. Topological analysis identified 10 hub targets (STAT1, STAT3, SRC, HCK, EGFR, SYK, PIK3CA, PIK3CB, PIK3R1, and PTPN11). Gene Ontology and KEGG pathway enrichment were performed with an FDR cut-off < 0.05. Significantly enriched pathways included JAK–STAT signaling, chemokine signaling, EGFR-TKI resistance, PI3K complex signaling, and viral infection pathways, particularly those related to Kaposi sarcoma virus and HSV-1, indicating immunoregulatory and antiviral roles. Molecular docking was performed using AutoDock Vina 1.1.2 to evaluate binding affinity and interaction mode of key PN phytochemicals against the hub proteins, and results were compared to their respective co-crystallized ligands. Results: Molecular docking indicated that major phytochemicals from PN exhibited significant binding affinities across all 10 hub host targets, typically outperforming or closely matching their respective co-crystallized ligands. The strongest contacts were observed for β-sitosterol–PIK3CB (−14.2 kcal/mol) and oleanolic acid–SYK (−14.0 kcal/mol), which were significantly stronger than the co-crystallized ligands (−7.9 and −8.3 kcal/mol, respectively), indicating robust stabilization within catalytic and regulatory pockets. Procyanidin B2 toward HCK (−10.5 vs. −7.9 kcal/mol) and PIK3CA (−9.5 vs. −7.3 kcal/mol), quercetin toward PIK3R1 (−10.6 vs. −8.2 kcal/mol) and PTPN11 (−9.2 vs. −7.5 kcal/mol), rutin toward SRC (−10.5 vs. 7.8 kcal/mol), and diosgenin toward EGFR (−9.4 vs. 8.4 kcal/mol). Procyanidin B2 maintained robust multi-hydrogen bonding networks, demonstrating significant binding, despite STAT1 and STAT3 docking showing identical affinities to co-crystals. Conserved hydrogen bonds, π–cation interactions, and significant hydrophobic packing at ATP-binding clefts and regulatory domains supported these interaction patterns, indicating competitive suppression of host signaling nodes taken over by HBV. Conclusions: Together, these results demonstrate that the components of PN possess strong multitarget binding capabilities across the PI3K/AKT, JAK–STAT, SRC-family kinase, EGFR, and SYK pathways, supporting their potential repurposing as host-directed HBV therapeutics with the ability to impede immune evasion, viral persistence, and HBV-associated oncogenic progression. Full article

K-Rev Interaction Trapped protein-1 (KRIT1) is a scaffold protein that forms functional protein complexes involved in physiologically important signaling networks. While it is primarily recognized for its association with Cerebral Cavernous Malformations (CCMs), KRIT1 may also play critical roles in tumor formation and the acquisition of malignant phenotypes, regulating cell adhesion, cytoskeletal dynamics, and angiogenesis. In this study, we investigated the role of KRIT1 in cancer cell migration and metastasis, with a focus on identifying novel interacting proteins and characterizing the intracellular signaling pathways activated upon its loss. By using a yeast two-hybrid screening, we identified Kinesin Family Member 1C (KIF1C), a protein involved in regulating podosome and invadopodium elongation, as a novel binding partner of KRIT1, and the interaction was confirmed in melanoma and epithelial cancer cells. In silico docking and interaction interface analyses supported the KRIT1–KIF1C interaction, providing structural insight into the binding mode as shown experimentally. We also found that SRC and focal adhesion kinase (FAK) phosphorylation, as well as Ras homolog family member A (RhoA) expression, represent additional pathways affected by the loss of KRIT1. This study confirms our earlier hypothesis that KRIT1 functions as a tumor suppressor and uncovers a compelling link between its loss and enhanced cancer aggressiveness. Full article

Background/Objectives: Epstein–Barr virus (EBV) is associated with a subset of gastric carcinomas characterized by latency programs that promote survival of infected cells. EBV-encoded BamH I A rightward transcript (BART) microRNAs contribute to apoptosis resistance in infected epithelial cells. This study investigated whether dasatinib, a Src family kinase (SFK) inhibitor, selectively targets EBV-positive gastric epithelial cells and examined the molecular mechanisms underlying this effect. Methods: EBV-positive and EBV-negative gastric epithelial cell models were analyzed to evaluate cell viability, apoptosis induction, signaling pathways, and viral gene regulation. BART miRNA expression was quantified by RT-qPCR, and promoter activity was examined using luciferase reporter assays. Downstream target gene expression was analyzed at both the transcript and protein levels. Recombinant EBV lacking BZLF1 or LMP2A was used to assess the contributions of lytic activation and LMP2A-associated signaling. Results: Dasatinib preferentially reduced viability and induced apoptosis in EBV-positive gastric epithelial cells compared with EBV-negative counterparts. Treatment suppressed phosphorylation of Src and ERK and reduced expression of the anti-apoptotic proteins BCL-xL and MCL1. Apoptosis was also observed in cells infected with LMP2A-deficient EBV, suggesting that the effect cannot be fully explained by inhibition of LMP2A-associated signaling. Dasatinib inhibited BART miRNA promoter activity and reduced pri-, pre-, and mature miR-BART levels, accompanied by increased expression of pro-apoptotic target genes including CASZ1a, OCT1, ARID2, TP53INP1, and DAB2. In parallel, dasatinib suppressed BZLF1 promoter activity without evidence of lytic reactivation. Conclusions: Dasatinib promotes apoptosis in EBV-positive gastric epithelial cells in association with coordinated suppression of SFK signaling and EBV-encoded BART miRNA expression, accompanied by derepression of pro-apoptotic cellular genes. These findings reveal a previously underappreciated vulnerability of EBV-positive epithelial cells and suggest that targeting host kinase signaling pathways that regulate viral microRNAs may represent a potential therapeutic strategy for EBV-associated malignancies. Full article

Receptor protein tyrosine phosphatases (RPTPs) are transmembrane enzymes that counterbalance protein tyrosine kinase activity by catalyzing the removal of phosphate groups from tyrosine residues on target proteins. Despite their critical roles in regulating cellular proliferation, adhesion, differentiation, and survival, RPTPs remain significantly understudied compared to their kinase counterparts. Contrary to early assumptions that PTPs function as constitutive housekeeping enzymes, emerging evidence demonstrates that RPTPs exhibit highly context-dependent roles in cancer, functioning as tumor suppressors or tumor promoters, or displaying dual activities depending on tissue type, cellular environment, and the specific signaling networks involved. This review provides a comprehensive analysis of RPTP structure, catalytic mechanisms, regulatory processes, and interactions with signaling effectors in cancer. Through a systematic examination of RPTP expression patterns across ten cancer types using Clinical Proteomic Tumor Analysis Consortium (CPTAC) and International Cancer Proteogenome Consortium (ICPC) datasets, we identify subfamily-specific and cancer-type-specific expression alterations that correlate with established functional classifications. PTPσ and PTPμ emerge as uniformly downregulated tumor suppressors across diverse malignancies, whereas PTPα and PTPε display oncogenic potential by activating Src family kinases. Context-dependent RPTPs, such as LAR and DEP-1, exhibit variable expression patterns that reflect their complex, multifaceted signaling roles. These findings establish RPTPs as critical regulators of cancer signaling with significant therapeutic potential while underscoring the need to understand tissue-specific signaling architectures when developing RPTP-targeted interventions. Full article

Src family tyrosine kinases regulate oocyte maturation and fertilization in many species, yet their physiological roles in Xenopus laevis (X. laevis) remain incompletely defined. Here, we generated three X. laevis Src (xSrc) constructs with defined point mutations allowing for selective immunochemical detection and controlled modulation of kinase activity: wild type (xSrcWT, Arg121His), constitutively active (xSrcKA, Arg121His/Tyr526Phe), and kinase-negative (xSrcKN, Arg121His/Lys294Met). Capped mRNAs were microinjected into immature oocytes, and effects on meiotic maturation and egg activation were analyzed. All constructs produced detectable Src protein within 4–5 h after injection without inducing progesterone-independent maturation. Following progesterone treatment, MAP kinase phosphorylation, CDK1 activation, and germinal vesicle breakdown (GVBD) occurred normally in all groups, although xSrcKA-expressing oocytes showed a modest but reproducible acceleration of MAPK activation and GVBD. Global tyrosine phosphorylation analysis revealed increased phosphorylation of several proteins, including a prominent ~50 kDa substrate, specifically in xSrcKA oocytes. After maturation, oocytes were subjected to artificial activation. xSrcKN-expressing oocytes responded normally to Ca²⁺ ionophore (A23187), indicating that Src activity is not required for direct Ca²⁺-mediated activation. In contrast, xSrcKN oocytes exhibited markedly reduced activation in response to hydrogen peroxide or Cathepsin B, which stimulate membrane-associated signaling pathways. These findings demonstrate that Src kinase activity is required for membrane signal-mediated egg activation but is dispensable for activation driven by direct intracellular Ca²⁺ elevation. Collectively, our results identify Src kinase as a positive regulator of progesterone-induced meiotic maturation and a critical mediator of specific fertilization-like activation pathways in X. laevis. Full article

Scaffold-aware artificial intelligence (AI) models enable systematic exploration of chemical space conditioned on protein-interacting ligands, yet the representational principles governing their behavior remain poorly understood. The computational representation of structurally complex kinase small molecules remains a formidable challenge due to the high conservation of ATP active site architecture across the kinome and the topological complexity of structural scaffolds in current generative AI frameworks. In this study, we present a diagnostic, modular and chemistry-first generative framework for design of targeted SRC kinase ligands by integrating ChemVAE-based latent space modeling, a chemically interpretable structural similarity metric (Kinase Likelihood Score), Bayesian optimization, and cluster-guided local neighborhood sampling. Using a comprehensive dataset of protein kinase ligands, we examine scaffold topology, latent-space geometry, and model-driven generative trajectories. We show that chemically distinct scaffolds can converge toward overlapping latent representations, revealing intrinsic degeneracy in scaffold encoding, while specific topological motifs function as organizing anchors that constrain generative diversification. The results demonstrate that kinase scaffolds spanning 37 protein kinase families spontaneously organize into a coherent, low-dimensional manifold in latent space, with SRC-like scaffolds acting as a structural “hub” that enables rational scaffold transformation. Our local sampling approach successfully converts scaffolds from other kinase families (notably LCK) into novel SRC-like chemotypes, with LCK-derived molecules accounting for ~40% of high-similarity outputs. However, both generative strategies reveal a critical limitation: SMILES-based representations systematically fail to recover multi-ring aromatic systems—a topological hallmark of kinase chemotypes—despite ring count being a top feature in our structural similarity metric. This “representation gap” demonstrates that no amount of scoring refinement can compensate for a generative engine that cannot access topologically constrained regions. By diagnosing these constraints within a transparent pipeline and reframing scaffold-aware ligand design as a problem of molecular representation our work provides a conceptual framework for interpreting generative model behavior and for guiding the incorporation of structural priors into future molecular AI architectures. Full article