Search Results (132)

CK2α and CK2α’, two paralogous members of the human kinome, are catalytic subunits of protein kinase CK2. Together with the regulatory subunit CK2β, they form heterotetrameric holoenzymes. CK2 is the subject of efforts to develop effective and selective inhibitors. For this, secondary binding sites remote from the canonical ATP/GTP cavity are critical. A crystallographic fragment screening with CK2α’ crystals and an established molecular fragment collection was performed to identify new ligands at known or novel sites. It resulted in fourteen CK2α’/fragment structures. Five fragments were found at the CK2β interface of CK2α’ and three fragments at the established αD pocket, which exhibits subtle differences between CK2α and CK2α’; comparative co-crystallisations with CK2α showed that one of them binds to the αD pocket of CK2α’ exclusively. No fragments bound at the substrate-binding region of CK2α’, but a CK2α’ structure with dp10, a decameric section of the substrate-competitive inhibitor heparin, and the indenoindole-type ATP-competitive inhibitor 4w was determined. A comparison with a published CK2α/dp10 structure revealed features consistent with reports about substrate specificity differences between the isoenzymes: dp10 binds to CK2α’ and CK2α with opposite strand orientations, and the local conformations of the isoenzymes in the helix αD region are significantly different. Full article

Background: Both clinical and research data support the contribution of IL6-mediated local immunosuppression coupled with IL6-initiated protumorigenic processes, e.g., sustained proliferation and angiogenesis in the development of many cancers, including lung cancer. By virtue of their pharmacologic advantage, controlled release, local delivery formulations can provide immunochemopreventive relevant agent levels at the target site with negligible systemic agent-related effects. Bioavailability is a major challenge with chemopreventive agents. Methods: Janus nanoparticles (JNPs), however, are a versatile drug delivery platform that addresses several major cancer preventive challenges including bioavailability and retention of bioactivity, with elimination of potential deleterious effects with systemic administration. Furthermore, JNPs feature two discrete compartments that enable concurrent delivery of two chemically distinct agents with complementary mechanisms of action. Results: Our data show that the synthetic vitamin A derivative, fenretinide (4HPR), and the IL6R inhibitor, tocilizumab (TCZ), inhibit pathways integral for the development of lung cancer. Initial molecular modeling and kinase activity assays confirmed that 4HPR serves as a competitive inhibitor for active-site ATP binding of two key IL6 downstream kinases (JAK1, CK2). Concurrent RNA-seq analyses that employed Qiagen Ingenuity Pathway Analysis showed significant inhibition of canonical pathways associated with DNA replication and division in conjunction with significant activation of immunogeneic cell death and TREM 1 signaling pathways and showed the immune-augmenting, cancer-preventive impact of 4HPR-TCZ treatment on gene expression in premalignant lung epithelial cells. Subsequent qRT-PCR analyses corroborated the RNA seq findings and demonstrated 3- to 6-fold increased expression of TREM 1 and immunogenic cell death genes, such as TREM1 and NLRC4 and HSPA6 and DDTT3, respectively. These data collectively guided the development of human serum albumin–chitosan JNPs for the co-delivery of 4HPR and TCZ, respectively. 4HPR-TCZ JNP characterization studies demonstrated high circularities and stability in suspension, as shown by consistency in diameter and minimal changes to the polydispersity index, while confocal microscopy confirmed their biocompartmental nature. Subsequent tertiary chemoprevention in vivo studies that employed a highly aggressive human lung cancer cell line showed that JNPs releasing 4HPR and 4HPR-TCZ significantly reduced tumor volume, as assessed by vital tumor tissue, suppressed proliferation, increased apoptosis, and promoted intratumor vascular instability. Conclusions: Collectively, these studies elucidate 4HPR-TCZ in vitro chemopreventive mechanisms of action and demonstrate proof of concept for JNP-4HPR-TCZ in vivo efficacy. Full article

Polo-like kinase 1 (PLK1) is a serine/threonine kinase that orchestrates multiple critical events during mitosis, including centrosome maturation, spindle assembly, kinetochore–microtubule attachment, and cytokinesis. Dysregulation and overexpression of PLK1 are frequently observed in various cancers, correlating with increased proliferation, metastatic potential, and poor prognosis, which highlights its potential as a therapeutic target. Traditional small-molecule inhibitors have predominantly focused on the ATP-binding site of the N-terminal kinase domain, effectively inducing mitotic arrest and apoptosis in tumor cells; however, these compounds often suffer from limited selectivity and off-target toxicity. The C-terminal Polo-box domain (PBD), responsible for substrate recognition and subcellular localization, has emerged as an alternative and highly selective target for inhibitor design, enabling the disruption of protein–protein interactions critical for PLK1 function. Here, we present a comprehensive review demonstrating the potential inhibition of several compounds against PLK1. This work establishes a foundation for future preclinical development of small molecule-based therapeutics against PLK1-dependent malignancies. Full article

The BCR-ABL1 fusion protein is a critical therapeutic target in Chronic Myeloid Leukemia (CML). Current monotherapy approaches involve types of inhibitors that can be categorized into ATP competitive inhibitors and allosteric inhibitors. However, resistance mutations in the tyrosine kinase domain of BCR-ABL1 have limited the effectiveness of these drugs. Research indicates that dual inhibition of BCR-ABL1 by combining these two types of inhibitors effectively addresses the issue of drug resistance as there are no overlapping resistance mechanisms. However, the underlying reasons for the observed synergistic effects have not yet been thoroughly elucidated. In this study, we employed molecular dynamics simulation to observe the synergistic interactions of BCR-ABL1 by the allosteric inhibitor asciminib and ATP competitive inhibitors nilotinib and ponatinib. Our study reveals that when asciminib binds to BCR-ABL1, nilotinib and ponatinib exhibit more substantial binding stability compared to monotherapy. At the atomic level, we have elucidated the reasons for the enhanced binding affinity of nilotinib and ponatinib when using a co-inhibition therapy. Our study reveals the allosteric communication pathway between asciminib and ponatinib, providing more detailed insights into the effectiveness of combination therapy. These findings provide valuable insights into combination therapies, aiding in the rational use of medications and guiding the design of novel inhibitors. Full article

The endoplasmic reticulum (ER) maintains protein homeostasis through chaperone-mediated folding and ER-associated degradation (ERAD). Disruption of this quality control, particularly involving the ER chaperone GRP94, contributes to diseases such as hypercholesterolemia, cancer, and immune disorders, where defective GRP94-dependent folding and the trafficking of client proteins like PCSK9, integrins, and Toll-like receptors drive pathology. Here, we characterize NSC637153 (cp153), a small molecule identified in a drGFP-based ERAD dislocation screen, as a selective probe of GRP94-dependent processes. cp153 inhibits the dislocation of ERAD substrates, preferentially affecting luminal clients, increases PCSK9 secretion, and promotes LDLR degradation. Unlike ATP-competitive HSP90 inhibitors, cp153 does not induce HSP70 or destabilize AKT, suggesting that it perturbs GRP94 function by interfering with client interaction or folding. The identification of cp153 provides a useful tool to for probing GRP94’s role in protein folding, trafficking, ER quality control, and disease-relevant signaling pathways, and supports the development of client-selective GRP94-targeted therapies. Full article

Phosphatidylinositol 3-kinase alpha (PI3Kα) is frequently mutated in head and neck squamous cell carcinoma (HNSCC), leading to the constitutive activation of the PI3K/Akt pathway, which promotes tumor cell proliferation, survival, and metastasis. PI3Kα allosteric inhibitors demonstrate therapeutic potential as both monotherapy and combination therapy, particularly in patients with PIK3CA mutations or resistance to immunotherapy, through the precise targeting of mutant PI3Kα. Compared to ATP-competitive PI3Kα inhibitors such as Alpelisib, the allosteric inhibitor RLY-2608 exhibits enhanced selectivity for mutant PI3Kα while minimizing the inhibition of wild-type PI3Kα, thereby reducing side effects such as hyperglycemia. To date, no allosteric PI3Kα inhibitors have been approved for clinical use. To develop novel PI3Kα inhibitors with improved safety and efficacy, we employed a scaffold hopping approach to structurally modify RLY-2608 and constructed a compound library. Based on the structural information of the PI3Kα allosteric site, we conducted the systematic virtual screening of 11,550 molecules from databases to identify lead compounds. Through integrated approaches, including molecular docking studies, target validation, druggability evaluation, molecular dynamics simulations, and metabolic pathway and metabolite analyses, we successfully identified a promising novel allosteric PI3Kα inhibitor, H-18 (3-(2-chloro-5-fluorophenyl)isoindolin-1-one). H-18 has not been previously reported as a PI3Kα inhibitor, and provides an excellent foundation for subsequent lead optimization, offering a significant starting point for the development of more potent PI3Kα allosteric inhibitors. Full article

Lyn is a multifunctional Src-family kinase (SFK) that regulates immune signaling and has been implicated in diverse types of cancer. Unlike other SFKs, its full-length structure and regulatory dynamics remain poorly characterized. In this study, we present the first long-timescale molecular dynamics analysis of full-length Lyn, including the SH3, SH2, and SH1 domains, across wildtype, ligand-bound, and cancer-associated mutant states. Using principal component analysis, dynamic cross-correlation matrices, and network-based methods, we show that ATP binding stabilizes the kinase core and promotes interdomain coordination, while the ATP-competitive inhibitor dasatinib and specific mutations (e.g., E290K, I364N) induce conformational decoupling and weaken long-range communication. We identify integration modules and develop an interface-weighted scoring scheme to rank dynamically central residues. This analysis reveals 44 allosteric hubs spanning SH3, SH2, SH1, and interdomain regions. Finally, a random forest classifier trained on 16 MD-derived features highlights key interdomain descriptors, distinguishing functional states with an AUC of 0.98. Our results offer a dynamic and network-level framework for understanding Lyn regulation and identify potential regulatory hotspots for structure-based drug design. More broadly, our approach demonstrates the value of integrating full-length MD simulations with network and machine learning techniques to probe allosteric control in multidomain kinases. Full article

Protein kinase CK2 has emerged as a pivotal regulator of cellular processes involved in skin homeostasis, including cell proliferation, differentiation and inflammatory response regulation. In fact, CK2 activity dysregulation is implicated in the pathogenesis of different skin diseases, such as psoriasis, cancer and inflammatory dermatoses. CK2 overactivation fosters keratinocyte proliferation and pro-inflammatory cytokine production through the STAT3 and Akt pathways in psoriasis, thus contributing to epidermal hyperplasia and inflammation. In the realm of oncology, CK2 overexpression correlates with tumor progression, facilitating cell survival and metastasis in melanoma and non-melanoma skin cancers. Pharmacological inhibition of CK2 has demonstrated therapeutic potential, with CX-4945 (Silmitasertib) as the most studied adenosine triphosphate-competitive inhibitor (ATP-competitive inhibitor). Preclinical models reveal that CK2 inhibitors effectively mitigate pathological features of psoriasis, regulate keratinocyte differentiation, and suppress tumor growth in skin cancers. These inhibitors also potentiate the efficacy of conventional chemotherapeutics and exhibit anti-inflammatory effects in dermatological conditions. Future research will aim to enhance the specificity and delivery of CK2-targeting therapies, including topical formulations, to minimize systemic side effects. Combination therapies integrating CK2 inhibitors with other agents might offer synergistic benefits in managing skin diseases. This review underscores CK2’s critical role in skin and its therapeutic potential as a pharmacological target, advocating for innovative approaches to harness CK2 inhibition in dermatology. Full article

Pyrazolo[1,5-a]pyrimidine is a nitrogen-containing fused heterocycle that imitates the nitrogenous base adenine with varying degrees of reliability. This fact determines its frequent use in drug design, including the development of ATP-competitive kinase inhibitors. These include dorsomorphin which shows compromised kinase selectivity but is still widely used as an AMPK inhibitor. ATP-binding pockets of many proteins have a fairly conservative spatial structure and there is a high probability of obtaining a compound with low target selectivity during drug development. In the case of a common scaffold, the careful selection of side substituents that determine the activity and selectivity of the final compound plays an important role. In this work, a convergent strategy for the synthesis of dorsomorphin and its close analogs was developed and implemented. The resulting small series of compounds is distinguished by the maximum possible diversification and allows for an assessment of the biological activity towards AMPK. An original route to obtain variants of the phenoxy-alkylamine moiety of dorsomorphin via the Mitsunobu reaction will be useful for generating targeted-focused libraries of ATP-competitive kinase inhibitors and highly active receptor ligands. Full article

Head and neck squamous cell carcinoma (HNSCC) remains a major health burden, with abnormal activation of phosphatidylinositol 3-kinase alpha (PI3Kα) strongly implicated in its pathogenesis. Targeting PI3Kα represents a promising therapeutic strategy. In this study, we employed structure-based virtual screening to identify natural small-molecule inhibitors of PI3Kα. A total of 12,800 molecules were screened, and five compounds were selected for further evaluation based on binding affinity and interaction patterns. Pharmacokinetic properties were assessed using ADMET predictions, and molecular dynamics (MD) simulations were conducted to validate the binding stability. Among the candidates, Apigetrin demonstrated favorable ADMET properties, a high safety profile, and stable binding within the ATP-binding pocket of PI3Kα. These findings suggest that Apigetrin is a promising natural PI3Kα inhibitor with potential therapeutic relevance for HNSCC. Full article

Despite the groundbreaking success of tyrosine kinase inhibitor therapy, the management of chronic myeloid leukemia patients is often impaired by resistance due to specific point mutations in the BCR::ABL1 oncogene. Upon classical ATP-competitive inhibitor treatment, these single nucleotide variants occur in the tyrosine kinase domain of ABL1. The novel allosteric BCR::ABL1 inhibitor asciminib was developed to treat CML patients alone or in combination to overcome or potentially prevent these treatment-emergent TKD mutations. Here, we present a case of a patient undergoing first-line asciminib therapy, and subsequently develop a specific BCR::ABL1/A337V point mutation, which resulted in asciminib resistance. Switching to second-line dasatinib treatment successfully overcame asciminib resistance and helped to achieve a deep molecular response. In case of treatment failures caused by single asciminib-specific point mutations, dasatinib therapy is a feasible choice. Full article

Background/Objectives: The mammalian target of the rapamycin (mTOR) signaling pathway is a central regulator of cell growth, proliferation, metabolism, and survival. Dysregulation of mTOR signaling contributes to many human diseases, including cancer, diabetes, and obesity. Therefore, inhibitors against mTOR’s catalytic kinase domain (KD) have been developed and have shown significant antitumor activities, making it a promising therapeutic target. The ATP–KD interaction is particularly important for mTOR to exert its cellular functions, and such inhibitors have demonstrated efficient attenuation of overall mTOR activity. Methods: In this study, we screened the Traditional Chinese Medicine (TCM) database, which enlists natural products that capture the relationships between drugs targets and diseases. Our aim was to identify potential ATP-competitive agonists that target the mTOR-KD and compete with ATP to bind the mTOR-KD serving as potential potent mTOR inhibitors. Results: We identified two compounds that demonstrated interatomic interactions similar to those of ATP–mTOR. The conformational stability and dynamic features of the mTOR-KD bound to the selected compounds were tested by subjecting each complex to 200 ns molecular dynamic (MD) simulations and molecular mechanics/generalized Born surface area (MM/GBSA) to extract free binding energies. We show the effectiveness of both compounds in forming stable complexes with the mTOR-KD, which is more effective than the mTOR-KD–ATP complex with more robust binding affinities. Conclusions: This study implies that both compounds could serve as potential therapeutic inhibitors of mTOR, regulating its function and, therefore, mitigating human disease progression. Full article

Background: The novel bacterial topoisomerase inhibitors (NBTIs) developed in our laboratory show potent on-target enzyme inhibition but suffer from low activity against Gram-negative bacteria. Methods: With the aim of improving the antibacterial activity of our compounds against Gram-negative bacteria, we tested them in combination with different efflux pump inhibitors (EPIs), a strategy that showed promise in several other classes of antimicrobials. We also investigated the combined effect of NBTIs with ATP-competitive inhibitors of bacterial type II topoisomerases (ACIs), as well as the antibiofilm properties of our compounds and the combination with EPIs against early and mature Acietobacter baumannii biofilm. Results: Our results demonstrate that combinations of NBTIs with EPI Phenylalanine-arginyl-β-naphthylamide significantly reduce the corresponding NBTIs’ minimal inhibitory concentration values and show potentiation of A. baumannii biofilm inhibition as compared to NBTIs alone. Although combinations of NBITs and ACIs did not show synergistic effects, the FIC index value calculations revealed additive effects for all the combinations of a selected NBTI in combination with three ACIs in all the assayed Gram-negative bacteria from the ESKAPE group. Conclusions: These results show for the first time that combinations of NBTIs with either EPIs or a different class of the topoisomerase inhibitors may be a beneficial strategy to combat difficult-to-treat bacterial infections. Full article

Subependymal giant cell astrocytoma (SEGA) is most often found in patients with TSC (Tuberous Sclerosis Complex). Although it has been classified as a benign tumor, it may create a serious medical problem leading to grave consequences, including young patient demise. Surgery and chemotherapy belong to the gold standard of treatment. A broader pharmacological approach involves the ever-growing number of rapalogs and ATP-competitive inhibitors, as well as compounds targeting other kinases, such as dual PI3K/mTOR inhibitors and CK2 kinase inhibitors. Novel approaches may utilize noncoding RNA-based therapeutics and are extensively investigated to this end. The purpose of our review was to characterize SEGA and discuss the latest trends in the diagnosis and therapy of this disease. Full article

Signaling proteins in eukaryotes usually comprise a catalytic domain coupled to one or several interaction domains, such as SH2 and SH3 domains. An additional class of proteins critically involved in cellular communication are adapter or scaffold proteins, which fulfill their purely non-enzymatic functions by organizing protein–protein interactions. Intriguingly, certain signaling enzymes, e.g., kinases and phosphatases, have been demonstrated to promote particular cellular functions by means of their interaction domains only. In this review, we will refer to such a function as "the adapter function of an enzyme". Though many stories can be told, we will concentrate on several proteins executing critical adapter functions in cells of the immune system, such as Bruton´s tyrosine kinase (BTK), phosphatidylinositol 3-kinase (PI3K), and SH2-containing inositol phosphatase 1 (SHIP1), as well as in cancer cells, such as proteins of the rat sarcoma/extracellular signal-regulated kinase (RAS/ERK) mitogen-activated protein kinase (MAPK) pathway. We will also discuss how these adaptor functions of enzymes determine or even undermine the efficacy of targeted therapy compounds, such as ATP-competitive kinase inhibitors. Thereby, we are highlighting the need to develop pharmacological approaches, such as proteolysis-targeting chimeras (PROTACs), that eliminate the entire protein, and thus both enzymatic and adapter functions of the signaling protein. We also review how genetic knock-out and knock-in approaches can be leveraged to identify adaptor functions of signaling proteins. Full article