FDA-approved small-molecule kinase inhibitors

Tracking protein kinase targeting advances: integrating QSAR into machine learning for kinase-targeted drug discovery

Protein kinases are vital drug targets, yet designing selective inhibitors is challenging, compounded by resistance and kinome complexity. This review explores Quantitative Structure-Activity Relationship (QSAR) modeling for kinase drug discovery, focusing on integrating traditional QSAR with machine learning (ML)-CNNs, RNNs-and structural data. Methods include structural databases, docking, and deep learning QSAR. Key findings show ML-integrated QSAR significantly improves selective inhibitor design for CDKs, JAKs, PIM kinases. The IDG-DREAM challenge exemplifies ML's potential for accurate kinase-inhibitor interaction prediction, outperforming traditional methods and enabling inhibitors with enhanced selectivity, efficacy, and resistance mitigation. QSAR combined with advanced computation and experimental data accelerates kinase drug discovery, offering transformative precision medicine potential. This review highlights deep learning-enhanced QSAR's novelty in automating feature extraction and capturing complex relationships, surpassing traditional QSAR, while emphasizing interpretability and experimental validation for clinical translation.

Room-Temperature Copper Cross-Coupling Reactions of Anilines with Aryl Bromides

We present a novel copper-catalyzed method for aniline cross-couplings promoted by a 6-hydroxy picolinhydrazide ligand. The method achieves room-temperature reactivity with aryl bromides, enabled by a methanol/ethanol solvent mixture and a mild, functional group-compatible base, with catalyst loadings as low as 0.5 mol %. The use of industrially preferred solvents and base, as well as the high catalytic activity, offers a significant advancement in the practicality and scalability of industrial processes. Furthermore, the approach extends to the cross-coupling of aryl chlorides under elevated temperatures and demonstrates compatibility with additional nucleophile classes.

Synthesis, Molecular Docking, and Biological Activity of New EGFR-Targeted Photosensitizers Based on Cationic Porphyrins Encapsulated into Pluronic F127 Micelles

The development of new effective photosensitizers (PS) for photodynamic therapy (PDT) is one of the important tasks in medical and organic chemistry. PSs inhibiting epidermal growth factor receptors (EGFR) overexpressed in cancer cells are of particular importance. In this work, we proposed the design and molecular docking of novel hybrid photosensitizers based on meso-aryl-substituted porphyrins and the Erlotinib molecule, a clinically approved tyrosine kinase inhibitor. The spacer length between the macrocycles and Erlotinib, hydrophilicity, and hydrophobicity of the porphyrin ring substituents were varied in the obtained compounds to evaluate structure-activity relationships (SAR). Photophysical and photochemical characteristics were studied for all of the received compounds in the presence of solubilizers suitable for the creation of dosage forms. Nanomicelles based on Pluronic F127 were obtained and characterized for the received compounds. In vitro biological tests on three cancer cell lines, MCF-7 (breast carcinoma), A431 (epidermoid carcinoma), MDA-MB-231 (breast adenocarcinoma), and normal NKE cells (human kidney epithelial cells) were performed, which showed low dark toxicity as well as light-induced activity of conjugates in the nanomolar range. Confocal microscopy experiments showed preferred accumulation of UB-2 and a lower accumulation of UB-3 PSs. In the case of UB-3, we observed a pronounced colocalization with early endosome antigen (EEA1). Also, cell apoptosis and inhibition of phosphorylation of EGFR were demonstrated for the UB-3 compound. Thus, the proposed design of targeting PS containing cationic pyridyl moieties and a linker between the porphyrin macrocycle and Erlotinib can contribute to antitumor PDT.

Structural Optimization and MD Simulation Study of Benzimidazole Derivatives as Potent Mutant FLT3 Kinase Inhibitors Targeting AML

Acute myeloid leukemia (AML) is an aggressive hematological malignancy with poor survival rates in adults, posing a significant economic burden. FMS-like tyrosine kinase 3 (FLT3) mutations are linked to poor prognosis in AML and resistance to clinically approved FLT3 inhibitors. Previously, we reported a novel benzimidazole-based FLT3 inhibitor, 4ACP, with nanomolar activities against FLT3-ITD and FLT3-TKD mutants, showing selective cytotoxicity against FLT3-ITD+ AML cell lines. In this study, we synthesized 31 derivatives by modifying the 4-acetamidophenyl group and varying substituents at N1-phenyl and C2 positions. We identified compound 21l (3-acetamidophenyl) as the most potent derivative (FLT3-TKD(D835Y) IC50 = 1.47 nM). Linking 21l to a solvent-accessible group yielded compound 22b, which exhibited a sub-nanomolar activity against FLT-TKD(D835Y) mutant with an IC50 value of 0.48 nM. Compound 22b showed preferential antiproliferative activities against MOLM-14, MV4-11, MOLM-14-D835Y, and MOLM-14-F691L AML cell lines with IC50 values of 16.1, 10.5, 26.5, and 160.3 nM, respectively. 22b induced dose-dependent inhibition of FLT3, ERK, STAT5, and S6 phosphorylation, G0/G1 cell-cycle arrest, and apoptotic cell death at low nanomolar concentrations in MOLM-14 and MOLM-14-D835Y cells. It was more selective for FLT3-dependent cell lines, showing about 80-fold selectivity toward FLT3-TKD(D835Y) over KIT, indicating relative safety and lower myelosuppression potential. The molecular dynamics study of 4ACP and 22b was conducted to explain the significant changes in activity resulting from subtle structural alterations. Altogether, these findings establish 22b as a potent mutant FLT3 inhibitor, warranting further investigation and optimization to target resistant AML.

Properties of FDA-approved small molecule protein kinase inhibitors: A 2025 update

Because of the deregulation of protein kinase action in many inflammatory diseases and cancer, the protein kinase family has become one of the most significant drug targets in the 21st century. There are 85 FDA-approved protein kinase antagonists that target about two dozen different enzymes and four of these drugs were approved in 2024 and a fifth was approved in 2025. Of these drugs, five target dual specificity protein kinases (MEK1/2), fourteen inhibit protein-serine/threonine protein kinases, twenty-one block nonreceptor protein-tyrosine kinases, and 45 target receptor protein-tyrosine kinases. The data indicate that 75 of these drugs are prescribed for the treatment of neoplasms. Seven drugs (abrocitinib, baricitinib, deucravacitinib, deuruxolitinib, ritlecitinib, tofacitinib, upadacitinib) are prescribed for the management of inflammatory diseases (atopic dermatitis, rheumatoid arthritis, psoriasis, alopecia areata, and ulcerative colitis). Of the 85 FDA-approved agents, about two dozen are used in the treatment of multiple diseases. The following four drugs received FDA approval in 2024 - deuruxolitinib (alopecia areata), ensartinib and lazertinib (non-small cell lung cancer), and tovorafenib (pediatric glioma) while mirdametinib was approved in 2025 for the treatment of type I neurofibromatosis (von Recklinghausen disease). Apart from netarsudil, temsirolimus, and trilaciclib, the approved protein kinase blockers are orally bioavailable. This article summarizes the physicochemical properties of all 85 FDA-approved small molecule protein kinase inhibitors including the molecular weight, number of hydrogen bond donors/acceptors, ligand efficiency, lipophilic efficiency, polar surface area, and solubility. A total of 39 of the 85 FDA-approved drugs have a least one Lipinski rule of 5 violation.

L-741626 inhibits hepatocellular carcinoma progression by targeting Ref-1 to suppress MAPK/ERK signalling pathway activity

Hepatocellular carcinoma (HCC) is a common and challenging malignancy of the digestive tract. Unfortunately, patients with advanced HCC frequently experience limited long-term benefits from current treatments, highlighting the critical need for innovative therapeutic agents. The discovery and development of new small-molecule compounds that target tumours have become crucial aspects of cancer research. In this study, we report on L-741626, a compound that has significant inhibitory effects on HCC. Both in vivo and in vitro experiments confirmed that L-741626 inhibited the growth of HCC by suppressing the MAPK/ERK signalling pathway. Molecular docking simulations and drug affinity responsive target stability assays further identified redox Factor 1 (Ref-1) as a target of L-741626. Ref-1 is overexpressed in HCC and is correlated with poor prognosis and high stage. Further studies demonstrated that Ref-1 interacts with CRAF, a crucial component of the MAPK/ERK signalling pathway. Knockdown of Ref-1 in HCC cells led to inhibition of the MAPK/ERK pathway. Sorafenib is a well-established targeted therapy for the treatment of HCC, with its primary antitumor mechanism being the inhibition of the MAPK/ERK signalling pathway. However, the presence of tumor stem cells is a key factor contributing to resistance to sorafenib. Our study demonstrates that L-741626 can suppress tumor stemness in HCC. The combination of L-741626 and sorafenib significantly enhances the sensitivity of HCC, resulting in increased tumoricidal effects. Our findings reveal a novel pharmacological effect of L-741626, which inhibits MAPK/ERK signalling activity in HCC by targeting Ref-1. Furthermore, L-741626 exhibits a synergistic effect when combined with sorafenib, suggesting a new potential approach for HCC treatment.

Advancing Src kinase inhibition: From structural design to therapeutic innovation - A comprehensive review

Src kinase, a non-receptor tyrosine kinase implicated in cellular signaling networks, plays a pivotal role in tumor progression and therapeutic resistance. Despite intensive research efforts spanning decades, no Src-selective kinase inhibitors have yet entered clinical use, highlighting the challenges in developing targeted therapeutics. Here we review recent advances in small-molecule Src inhibitor development, focusing on structural design strategies, binding mechanisms, and therapeutic applications. We analyze emerging approaches including fragment-based drug design, allosteric targeting, and substrate-competitive inhibition that have yielded promising new scaffold classes. Special attention is given to innovations in achieving isozyme selectivity, particularly through exploitation of non-ATP binding pockets and covalent inhibition strategies. Integration of artificial intelligence, living organoid platforms, and targeted protein degradation technologies is accelerating inhibitor optimization. We discuss key challenges in Src inhibitor development, including the need for enhanced selectivity, reduced off-target effects, and improved resistance profiles. Our analysis reveals promising directions for future therapeutic development, emphasizing the importance of rational design principles guided by structural insights and emerging technologies. These findings provide a framework for developing next-generation Src inhibitors with improved clinical potential.

Synthesis of thiazoloquinolinone derivatives: molecular docking, MD simulation, and pharmacological evaluation as VEGFR-2 inhibitors

We synthesized a series of novel thiazoloquinolinone derivatives, achieving moderate to high yields ranging from 74 to 96%, and assessed their efficacy against Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) using in silico methodologies. The structures of these compounds were characterized through various spectroscopic techniques, including 1H-NMR, 13C-NMR, IR, and mass spectrometry. Comprehensive computational analyses, encompassing molecular docking, molecular dynamics (MD) simulations, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling, were conducted. Docking studies with VEGFR-2 revealed that all synthesized compounds exhibited docking scores between - 3.24 and - 6.63, indicating varying degrees of binding affinity. Notably, compound (5e) demonstrated the strongest binding affinity with an energy of - 6.63 kcal/mol. The MD simulations indicated that Lys868 was one of the amino acids exhibiting the highest frequency of interaction throughout the simulation. Analysis of the ADMET and physicochemical properties revealed that all inhibitor compounds possess favorable pharmacological characteristics.

Unveiling novel type 1 inhibitors for targeting LIM kinase 2 (LIMK2) for cancer therapeutics: An integrative pharmacoinformatics approach

LIMK2 is crucial in regulating actin cytoskeleton dynamics, significantly contributing to cancer cell proliferation, invasion, and metastasis. Inhibitors like LIMKi3 effectively suppress LIMK2 kinase activity by directly affecting actin polymerization and preventing the formation of structures like filopodia and lamellipodia, which are typical of motile cancer cells. By modulating these actin dynamics, LIMKi3 inhibits cancer cell migration and invasion, reducing the potential for metastasis. Thus, this study aims to explore potential anti-cancer therapeutic LIMK2 inhibitors with properties resembling LIMKi3. Henceforth, molecular docking was utilized in this study to comprehend the ATP mimetic binding mode of LIMKi3, followed by Pharmacophore-based virtual screening to identify small molecules resembling LIMKi3. In addition, molecular dynamics simulations were performed to explore the dynamic behavior of LIMK2 and potential inhibitors. Further, network analysis and binding free energy calculations were implemented to comprehensively assess the interactions between the compounds and LIMK2. In molecular docking, LIMKi3 demonstrated an ATP mimetic hinge binding mode with hydrogen bonds at Ile408. Among the screened compounds (NCI300395, ChemDiv-8020-2508, and ChemDiv-7997-0024), three displayed "ADRH" pharmacophoric features like LIMKi3, with favorable ADMET properties, higher binding affinity, and significant hydrogen bond interactions at Ile408. LIMK2-inhibitor complexes showed lower RMSD than LIMK2-LIMKi3, indicating higher equilibrium by identified compounds. Protein-drug Complexes exhibited significant inter-domain correlation in N-lobe residues of LIMK2, including conserved β3, αC, and Hinge residues. Binding free energy analysis ranked LIMK2-NCI300395 highest, followed by LIMK2-ChemDiv-7997-0024 and LIMK2-ChemDiv-8020-2508, highlighting their potential as effective LIMK2-targeting compounds. Hence, this study emphasizes LIMKi3's significance and identifies potential candidates (NCI300395, ChemDiv-7997-0024, and ChemDiv-8020-2508) for developing cancer therapeutics targeting LIMK2. These findings open avenues for further investigations into the complex interplay between cytoskeletal dynamics and cancer progression.

Design, Synthesis, and Biological Evaluation of Novel Fms-Like Tyrosine Kinase 3/VEGFR2/Histone Deacetylase Inhibitors for the Treatment of Acute Myeloid Leukemia

The concurrent targeting of Fms-like tyrosine kinase 3 (FLT3)/VEGFR2/Histone deacetylase (HDAC) represents a novel and promising therapeutic strategy for acute myeloid leukemia. In this work, we hybridized essential pharmacophores from sorafenib and SAHA (vorinostat) and then conducted structure-activity relationship studies to identify two lead compounds 26 and 32 that potently inhibit FLT3, VEGFR2, and HDAC in a nanomolar range. In cell evaluation, compounds 26 and 32 exhibited potent proliferative activities against a panel of leukemia cells including MV4-11 and MOLM-13. Western blotting analysis also showed that compounds 26 and 32 suppressed the phosphorylation of FLT3, STAT3, and ERK1/2 and increased histone H3 acetylation in a dose-dependent manner, indicating the effective inhibition of FLT3, VEGFR2, and HDAC. Supported by its pharmacokinetic properties, compound 26 showed remarkable anticancer efficacy in a MV4-11 xenograft model. Additionally, it demonstrated superior efficacy compared to midostaurin and gilteritinib in the Ba/F3-FLT3-ITD-N701K xenograft model.

Inferring kinase-phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets

Phosphorylation in eukaryotic cells plays a key role in regulating cell signaling and disease progression. Despite the ability to detect thousands of phosphosites in a single experiment using high-throughput technologies, the kinases responsible for regulating these sites are largely unidentified. To solve this, we collected the quantitative data at the transcriptional, protein, and phosphorylation levels of 10 159 samples from 23 tumor datasets and 15 adjacent normal tissue datasets. Our analysis aimed to uncover the potential impact and linkage of kinase-phosphosite (KPS) pairs through experimental evidence in publications and prediction tools commonly used. We discovered that both experimentally validated and tool-predicted KPS pairs were enriched in groups where there is a significant correlation between kinase expression/phosphorylation level and the phosphorylation level of phosphosite. This suggested that a quantitative correlation could infer the KPS interconnections. Furthermore, the Spearman's correlation coefficient for these pairs were notably higher in tumor samples, indicating that these regulatory interactions are particularly pronounced in tumors. Consequently, building on the KPS correlations of different datasets as predictive features, we have developed an innovative approach that employed an oversampling method combined with and XGBoost algorithm (SMOTE-XGBoost) to predict potential kinase-specific phosphorylation sites in proteins. Moreover, the computed correlations and predictions of kinase-phosphosite interconnections were integrated into the eKPI database (https://ekpi.omicsbio.info/). In summary, our study could provide helpful information and facilitate further research on the regulatory relationship between kinases and phosphosites.

Calothrixin B by docking JAK2 is a potential therapeutic inhibitor for pancreatic ductal adenocarcinoma

OBJECTIVES

Pancreatic cancer, a highly invasive and prognostically unfavorable malignant tumor, consistently exhibits resistance to conventional chemotherapy, leading to substantial side effects and diminished patient quality of life. This highlights the critical need for the discovery of novel, effective, and safe chemotherapy drugs. This study aimed to explore bioactive compounds, particularly natural products, as an alternative for JAK2 protein inhibitor in cancer treatment.

METHODS

Molecular docking, molecular dynamics, and Western blot experiments were conducted to verify the binding of Calothrixin B to JAK2 and its inhibitory effect on the JAK2-STAT3 signaling axis.

KEY FINDINGS

Recognizing the significant impact of JAK-STAT3 signaling pathway in pancreatic cancer, we screened the Zinc database to discover potential JAK2 inhibitors, and identified the small molecule Calothrixin B as a promising drug. Molecular simulations revealed stable interactions and the formation of hydrogen bonds between Calothrixin B and specific amino acids (Asp 994, Leu 855, and Arg 980) after a 100 ns simulation. Furthermore, we show that Calothrixin B inhibited the activity of the JAK2-STAT3 signaling pathway, arrested pancreatic cancer cells in the G1 phase, induced apoptosis, and significantly inhibited cell migration. Moreover, in vivo on a subcutaneous tumor model in nude mice confirmed that Calothrixin B effectively inhibited tumor growth in nude mice. In addition, the combination of Carlothrixin B and gemcitabine had a better inhibitory effect on pancreatic cancer cells.

CONCLUSION

These findings introduce new avenues for Calothrixin B as promising therapy for pancreatic cancer.

Comprehensive multi-omics analysis elucidates colchicine-induced toxicity mechanisms and unveils the therapeutic potential of MLN4924 and kinase inhibitors

Colchicine is a widely prescribed anti-inflammatory drug for the treatment of gout, familial Mediterranean fever and pericarditis, but its narrow therapeutic window presents a significant risk of severe toxicity. Despite its clinical relevance, the molecular mechanisms underlying colchicine's pharmacological effects and associated toxicity and explored potential therapeutic interventions to mitigate its adverse effects. We showed the colchicine's impact on cellular morphology in human umbilical vein endothelial cells (HUVEC) and HeLa cells including cell rounding and detachment following 24 h of exposure that revealed pronounced cytotoxic effects. We then established a large-scale screening model to identify small molecules capable of reversing colchicine-induced cellular toxicity, and identified MLN4924, an inhibitor of the Cullin-RING E3 ligase (CRL) system, as a promising candidate for mitigating colchicine-induced cellular injury. Through a comprehensive multi-omics approach including transcriptomics, proteomics, phosphoproteomics and ubiquitinomics, we systematically characterized the molecular perturbations caused by colchicine and delineated the protective mechanisms of MLN4924. We found that MLN4924 exerted its protective effects by modulating critical cellular pathways, specifically preventing the dysregulation of cell cycle progression, mitotic disruption and microtubule destabilization triggered by colchicine. Furthermore, proteomic and phosphoproteomic analyses revealed significant alterations in kinase signaling networks, with combined inhibition of CDK1 and PAK1 emerging as an effective strategy to counteract colchicine-induced cellular dysfunction. These results not only provide a detailed molecular characterization of colchicine toxicity but also identify key therapeutic targets, laying the groundwork for the development of targeted interventions to mitigate colchicine-induced adverse effects in clinical practice.

The role of YTHDF2 in anti-tumor immunity

RNA N 6-methyladenosine (m6A) modification has been identified as the most abundant RNA modification and plays crucial roles in both physiological and pathological processes. YTHDF2 was the first identified reader protein that can recognize m6A modification and recent studies also revealed its ability to bind 5-methylcytidine (m5C) modification. YTHDF2 shows a dual binding capacity to both m6A and m5C, which leads to opposite mRNA outcomes. Multiple studies have highlighted the critical roles of YTHDF2 in tumor development and tumor microenvironment. Emerging findings showed that YTHDF2 plays critical roles in immune regulation, impacting T cell, B cell, NK cell, macrophage, innate/adaptive anti-tumor immune responses, and T-cell based immunotherapy. Inhibitors have been developed to target YTHDF2, which showed potential efficacy in tumor treatment. Herein, we reviewed the molecular mechanism of YTHDF2 and its roles in tumors, immune cells, and tumor microenvironment.

Advancements in proteogenomics for preclinical targeted cancer therapy research

Advancements in molecular characterization technologies have accelerated targeted cancer therapy research at unprecedented resolution and dimensionality. Integrating comprehensive multi-omic molecular profiling of a tumor, proteogenomics, marks a transformative milestone for preclinical cancer research. In this paper, we initially provided an overview of proteogenomics in cancer research, spanning genomics, transcriptomics, and proteomics. Subsequently, the applications were introduced and examined from different perspectives, including but not limited to genetic alterations, molecular quantifications, single-cell patterns, different post-translational modification levels, subtype signatures, and immune landscape. We also paid attention to the combined multi-omics data analysis and pan-cancer analysis. This paper highlights the crucial role of proteogenomics in preclinical targeted cancer therapy research, including but not limited to elucidating the mechanisms of tumorigenesis, discovering effective therapeutic targets and promising biomarkers, and developing subtype-specific therapies.

Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins

Knowledge of the structures formed by proteins and small molecules is key to understand the molecular principles of chemotherapy and for designing new and more effective drugs. During the early stage of a drug discovery program, it is customary to predict ligand-protein complexes in silico, particularly when screening large compound databases. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology to generate bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites by exploiting only information on the unbound structure and the putative binding sites. The protocol is validated on the paradigm enzyme adenylate kinase, for which we generated a significant fraction of bound-like structures. A fraction of these conformations, employed in ensemble-docking calculations, allowed to find native-like poses of substrates and inhibitors (binding to the active form of the enzyme), as well as catalytically incompetent analogs (binding the inactive form). Our protocol provides a general framework for the generation of bound-like conformations of challenging drug targets that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening, in the prediction of the impact of amino acid mutations on structure and dynamics, and in protein engineering.

Src inhibition potentiates MCL-1 antagonist activity in acute myeloid leukemia

The importance of MCL-1 in leukemogenesis has prompted development of MCL-1 antagonists e.g., S63845, MIK665. However, their effectiveness in acute myeloid leukemia (AML) is limited by compensatory MCL-1 accumulation via the ubiquitin proteasome system. Here, we investigated mechanisms by which kinase inhibitors with Src inhibitory activity e.g., bosutinib (SKI-606) might circumvent this phenomenon. MCL-1 antagonist/SKI-606 co-administration synergistically induced apoptosis in diverse AML cell lines. Consistently, Src or MCL-1 knockdown with shRNA markedly sensitized cells to MCL-1 inhibitors or SKI-606 respectively, while ectopic MCL-1 expression significantly diminished apoptosis. Mechanistically, MCL-1 antagonist exposure induced MCL-1 up-regulation, an event blocked by Src inhibitors or Src shRNA knock-down. MCL-1 down-regulation was associated with diminished transcription and increased K48-linked degradative ubiquitination. Enhanced cell death depended functionally upon down-regulation of phosphorylated STAT3 (Tyr705/Ser727) and cytoprotective downstream targets c-Myc and BCL-xL, as well as BAX/BAK activation, and NOXA induction. Importantly, the Src/MCL-1 inhibitor regimen robustly killed primary AML cells, including primitive progenitors, but spared normal hematopoietic CD34+ cells and human cardiomyocytes. Notably, the regimen significantly improved survival in an MV4-11 cell xenograft model, while reducing tumor burden in two patient-derived xenograft (PDX) AML models and increased survival in a third. These findings argue that Src inhibitors such as SKI-606 potentiate MCL-1 antagonist anti-leukemic activity in vitro and in vivo by blocking MCL-1 antagonist-mediated cytoprotective MCL-1 accumulation by promoting degradative ubiquitination, disrupting STAT-3-mediated transcription, and inducing NOXA-mediated MCL-1 degradation. They also suggest that this strategy may improve MCL-1 antagonist efficacy in AML and potentially other malignancies.

Salt-inducible kinase 2 confers radioresistance in colorectal cancer by facilitating homologous recombination repair

Resistance to radiotherapy remains a critical barrier in treating colorectal cancer (CRC), particularly in cases of locally advanced rectal cancer (LARC). To identify key kinases involved in CRC radioresistance, we employed a kinase-targeted CRISPR-Cas9 library screen. This approach aimed to identify potential kinase inhibitors as radiosensitizers. Our screening identified salt-inducible kinase 2 (SIK2) as a critical factor in CRC radioresistance. Increased SIK2 expression correlated with reduced tumor regression and poorer outcomes in LARC patients undergoing neoadjuvant chemoradiotherapy. The depletion of SIK2 significantly enhanced radiation-induced apoptosis and tumor regression. Mechanistically, SIK2 interacts with valosin-containing protein (VCP), promoting its hyperphosphorylation. This modification improves VCP's capacity to extract K48-linked ubiquitin-conjugated proteins from chromatin, thus aiding the recruitment of RPA and RAD51 to DNA damage sites. This mechanism strengthens homologous recombination-mediated DNA repair, which contributes to radioresistance. Importantly, ARN-3236, a SIK2 inhibitor, markedly sensitized CRC cells to radiation both in vivo and in vitro, providing a potential strategy to overcome radioresistance. In summary, our findings reveal a novel mechanism by which SIK2 contributes to the radioresistance of CRC, proposing SIK2 as a potential therapeutic target with its inhibitor significantly enhancing CRC radiotherapy efficacy.

Harnessing allosteric inhibition: prioritizing LIMK2 inhibitors for targeted cancer therapy through pharmacophore-based virtual screening and essential molecular dynamics

The therapeutic potential of small molecule kinase inhibitors in cancer treatment is well recognized. However, achieving selectivity remains a formidable challenge, primarily due to the structural similarity of ATP binding pockets among kinases. Allosteric inhibition, which involves targeting binding pockets beyond the ATP-binding site, provides a promising alternative to overcome this challenge. In this study, a meticulous approach was implemented to prioritize type 3 inhibitors for LIMK2, employing a range of techniques including Molecular Dynamics (MD) simulations, e-pharmacophore-guided High Throughput Virtual Screening (HTVS), MM/GBSA and ADMETox analyses, Density Functional Theory (DFT) calculations, and MM/PBSA investigations. The e-pharmacophore model identifies a hypothesis featuring five essential pharmacophoric elements (RRRAH). Through virtual screening of the ZINC compound database, we identified only five compounds that align with all four pharmacophoric features: ZINC1044382792, ZINC1433610865, ZINC1044109145, ZINC952869440, and ZINC490621334. These compounds not only exhibit higher binding affinity but also demonstrate favorable ADME/Tox profiles. Molecular dynamics simulations underscore the stability of hydrogen bond interactions with critical cryptic LIMK2 pocket residues, Asp469 and Arg474, only for two compounds: ZINC143361086 and ZINC1044382792. These compounds also exhibit superior occupancy interactions, as indicated by HOMO-LUMO analysis. Additionally, binding free energy calculations highlight the significant affinities of these two compounds when complexed with LIMK2: -83.491 ± 1.230 kJ/mol and -90.122 ± 1.248 kJ/mol for ZINC1044382792 and ZINC1433610862, respectively. Hence, this comprehensive investigation identifies ZINC1433610862 and ZINC1044382792 as prospective hits, representing promising leads for targeting LIMK2 in cancer therapeutics.Communicated by Ramaswamy H. Sarma.

YTHDF2 promotes ATP synthesis and immune evasion in B cell malignancies

Long-term durable remission in patients with B cell malignancies following chimeric antigen receptor (CAR)-T cell immunotherapy remains unsatisfactory, often due to antigen escape. Malignant B cell transformation and oncogenic growth relies on efficient ATP synthesis, although the underlying mechanisms remain unclear. Here, we report that YTHDF2 facilitates energy supply and antigen escape in B cell malignancies, and its overexpression alone is sufficient to cause B cell transformation and tumorigenesis. Mechanistically, YTHDF2 functions as a dual reader where it stabilizes mRNAs as a 5-methylcytosine (m5C) reader via recruiting PABPC1, thereby enhancing their expression and ATP synthesis. Concomitantly, YTHDF2 also promotes immune evasion by destabilizing other mRNAs as an N6-methyladenosine (m6A) reader. Small-molecule-mediated targeting of YTHDF2 suppresses aggressive B cell malignancies and sensitizes them to CAR-T cell therapy.

Structure-Based Rational Design and Evaluation of BET-Aurora Kinase Dual-Inhibitors for Treatment of Cancers

Simultaneous inhibition of the bromodomain and extra-terminal domain and Aurora kinases is a promising anticancer therapeutic strategy. Based on our previous study on BET-kinase dual inhibitors, we employed the molecular docking approach to design novel dual BET-Aurora kinase A inhibitors. Through several rounds of optimization and with the guidance of the solved cocrystal structure of BRD4 bound to inhibitor 27, we finally obtained a series of highly potent dual BET-Aurora kinase A inhibitors. Compound 38 exhibited strong affinity toward both BRD4 and Aurora kinase A. It also showed good antiproliferative activities on diverse cancer cell lines, good pharmacokinetic profiles, and favorable antitumor efficacy in renal cell cancer and colon cancer xenograft models with TGI of 45.99% and 53.06%, respectively. The development of compound 38 reinforces the concept that a rational design may achieve dual inhibitors targeting specific kinases and bromodomain proteins.

Design, synthesis, and X-ray structural studies of a series of highly potent, selective, and drug-like G protein-coupled receptor kinase 5 inhibitors

G protein-coupled receptor kinase 5 (GRK5) has emerged as a potential drug development target against heart failure and cancer. A close homolog, GRK6 represents a therapeutic target for multiple myeloma. We have rationally designed a series of highly selective, potent, noncovalent, and drug-like GRK5 inhibitors. Several inhibitors exhibited low nanomolar GRK5 inhibition and high selectivity over GRK2, and, surprisingly, some were selective for GRK6. We determined high-resolution X-ray crystal structures of several inhibitors in complex with GRK5, which provide molecular insights into the ligand-binding site interactions responsible for GRK5 selectivity and potency.

Tyrosine Kinase Inhibitor Induced Proteinuria - A Review

Tyrosine Kinase inhibitor (TKI) is a class of drugs that interfere with protein kinases' signal transduction pathways through an array of inhibitory mechanisms. Tyrosine kinases (TK) have an inevitable role in downstream signal transduction and the proliferation of tumour cells. Hence, tyrosine kinase inhibitors (TKIs) are frequently employed as anti-neoplastic agents in the treatment of colon, breast, kidney, and lung cancers. They can be used as single or combination therapy with other targeted therapies. It is understood that TKIs pose a risk of developing proteinuria in some patients as it can primarily result in dysfunction of the split diaphragm, constriction or blockage of capillary lumens mediated by the basement membrane, acute interstitial nephritis, or acute tubular necrosis. This paper reviews the mechanism of action of TKIs, the pathophysiological mechanism of TKI-induced proteinuria, and its management Fig. 1.

Regulation and signaling of the LIM domain kinases

The LIM domain kinases (LIMKs) are important actin cytoskeleton regulators. These proteins, LIMK1 and LIMK2, are nodes downstream of Rho GTPases and are the key enzymes that phosphorylate cofilin/actin depolymerization factors to regulate filament severing. They therefore perform an essential role in cascades that control actin depolymerization. Signaling of the LIMKs is carefully regulated by numerous inter- and intra-molecular mechanisms. In this review, we discuss recent findings that improve the understanding of LIM domain kinase regulation mechanisms. We also provide an up-to-date review of the role of the LIM domain kinases, their architectural features, how activity is impacted by other proteins, and the implications of these findings for human health and disease.

Psoriasis Risk With Immune Checkpoint Inhibitors

Importance

Immune checkpoint inhibitors (ICIs) are recognized as revolutionary cancer therapies but have raised concerns about immune-related adverse events, including the development of autoimmune diseases.

Objective

To evaluate the psoriasis risk associated with the use of ICIs in patients with cancer.

Design, Setting, and Participants

This nationwide cohort study with a target trial emulation design used data from the Taiwan National Health Insurance database and the Taiwan Cancer Registry. The participants included were patients who received antineoplastic medications for cancer at stages III and IV between January 1, 2019, and June 30, 2021. Data were analyzed from May 2023 to July 2024.

Exposures

Patients treated with ICIs were classified as ICI users, while those who received chemotherapy or targeted therapies were categorized as non-ICI users.

Main Outcome and Measures

The primary outcome was the incidence of psoriasis during the follow-up period. Stabilized inverse probability of treatment weighting (IPTW) was used to mitigate potential confounders. Cox and Fine-Gray hazard models were used to calculate hazard ratios (HRs) for psoriasis risk between groups.

Results

Of 135 230 patients who received antineoplastic medications (mean [SD] age, 62.94 [13.01] years; 45.1% female), 3188 patients were eligible for the ICI user group, while 132 042 patients were eligible for the non-ICI user group. ICI users experienced a higher incidence of psoriasis at 5.76 cases per 1000 person-years, compared to 1.44 cases in the non-ICI group. After adjusting for demographics and comorbidities, ICI users were found to have a 2-fold increase in the risk of developing psoriasis (IPTW-adjusted HR, 3.31; IPTW-adjusted subdistribution HR, 2.43). Both as-started design and on-treatment design showed consistent findings, and the results were consistent and robust across all follow-up intervals and all sensitivity analyses.

Conclusions and Relevance

In this cohort study, patients with cancer treated with ICIs faced an increased risk of psoriasis. Medical professionals should be aware of the potential adverse effects of immunotherapy to ensure optimal cancer care.

Structure activity relationship for anticancer activities of spirooxindole derivatives: A comprehensive review

Cancer remains one of the leading causes of mortality worldwide, necessitating the continuous search for novel therapeutic agents. Spirooxindole derivatives have recently emerged as a class of compounds with significant potential for cancer treatment owing to their diverse pharmacological activities and unique structural features. The structural diversity of spirooxindole derivatives enables a wide range of modifications, facilitating optimization of their pharmacokinetic and pharmacodynamic properties. Moreover, their ability to interact with multiple molecular targets involved in cancer progression, including kinases, receptors, and enzymes, makes them attractive candidates for multi-targeted therapy. In preclinical studies, numerous spirooxindole derivatives have demonstrated promising antiproliferative activity against various cancer cell lines, including breast, lung, colon, and prostate cancers. Mechanistic investigations have revealed their ability to induce cell cycle arrest and apoptosis and inhibit angiogenesis and metastasis, underscoring their potential as effective anticancer agents. However, challenges such as off-target effects, drug resistance, and limited bioavailability need to be addressed to maximize the therapeutic potential of these compounds. Continued research efforts to elucidate their molecular mechanisms, optimize their pharmacological properties, and conduct rigorous clinical evaluations are warranted to harness their full therapeutic benefits for cancer treatment. This review provides a comprehensive overview of recent advancements in developing spirooxindole derivatives as anticancer agents with structure-activity relationships.

Kinase-Bench: Comprehensive Benchmarking Tools and Guidance for Achieving Selectivity in Kinase Drug Discovery

Developing selective kinase inhibitors remains a formidable challenge in drug discovery because of the highly conserved structural information on adenosine triphosphate (ATP) binding sites across the kinase family. Tailoring docking protocols to identify promising kinase inhibitor candidates for optimization has long been a substantial obstacle to drug discovery. Therefore, we introduced "Kinase-Bench," a pioneering benchmark suite designed for an advanced virtual screen, to improve the selectivity and efficacy of kinase inhibitors. Our comprehensive data set includes 6875 selective ligands and 422,799 decoys for 75 kinases, using extensive bioactivity and structural data from the ChEMBL database and decoys generated by the Directory of Useful Decoys-Enhanced version. Our benchmarking sets and retrospective case studies were designed to provide useful guidance in discovering selective kinase inhibitors. We employed a Glide High-Throughput Virtual Screen and Standard Precision complemented by three scoring functions and customized protein-ligand interaction filters that target specific kinase residue interactions. These innovations were successfully implemented in our virtual screen efforts targeting JAK1 inhibitors, achieving selectivity against its family member, TYK2. Consequently, we identified novel potential hits: Compound 2 (JAK1 IC50: 980.5 nM, TYK2 IC50: 4.5 μM) and the approved pan-AKT inhibitor Capivasertib (JAK1 IC50: 275.9 nM, TYK2 IC50: 10.9 μM). Using the Kinase-Bench protocol, both compounds demonstrated substantial JAK1 selectivity, making them strong candidates for further investigation. Our pharmaceutical results underscore the utility of tailored virtual screen protocols in identifying selective kinase inhibitors with substantial implications for rational drug design. Kinase-Bench offers a robust toolset for selective kinase drug discovery with the potential to effectively guide future therapeutic strategies effectively.

Developing new anticancer agents: Design, synthesis, biological evaluation and in silico study of several functionalized pyrimidine-5-carbonitriles as small molecules modulators targeting breast cancer

Committed to our growing effort addressed toward the development of potent anti-breast cancer candidates, new 4-hydrazinylpyrimidine-5-carbonitriles featuring a morpholinyl or piperidinyl moiety at the position-2 and derivatized with various functionalities at the hydrazinyl group were designed through structure optimization, and their antiproliferative potency against two human breast cancer (BC) cell lines, relative to the reference drug 5-FU, was evaluated. Compounds showing remarkable cytotoxic activity versus the hormone dependent MCF-7 cell line (IC50 = 1.62 ± 0.06 µM- 9.88 ± 0.38 µM) and the non-hormone dependent MDA-MB-231 cell line (IC50 = 3.26 ± 0.14 µM-12.93 ± 0.55 µM) were further tested by multiple assays for clarification of their potential activity. Promising derivatives revealing low damage to healthy cells were subject to enzymatic inhibitory assessment against ARO and EGFR and their activities compared to letrozole and erlotinib respectively. Compounds 3c, 6a as well as compounds 4c, 4d proved to be good inhibitors of the ARO and EGFR enzymes respectively. Active compounds were also evaluated for their underlying mode of action by further investigation for CDK, Hsp90, PI3K inhibition and compared to normal MCF-10A cells and assessed for their enhancement of the caspase 9 levels. Additionally, cell cycle analysis and apoptotic induction were performed. They demonstrated remarkable activities in the previous assays and emanated as leads as anti-breast cancer candidates. Eventually, molecular docking analysis revealed that hit compounds 3c, 4c, 4d, and 6a could bind favorably to the proposed in silico models of various protein-ligand interactions. Therefore, our promising top candidates, by demonstrating appreciable anti-breast cancer activities, present valuable prospects for optimization, potency enhancement and future application.

Research progress on anti-tumor mechanism of TAOK kinases

Thousand and one amino-acid protein kinases(TAOKs), as a key member of the mitogen-activated protein kinase (MAPK) cascade, has recently attracted widespread attention in the field of anti-cancer research. There are three members of this subfamily: TAOK1, TAOK2, and TAOK3. Studies have shown that members of the TAOK family participate in regulating cell proliferation, apoptosis, migration, and invasion through various pathways, thereby playing an important role in tumorigenesis and progression. This review summarizes the functions of TAOK kinases in tumor cell signal transduction, cell cycle regulation, and the tumor microenvironment, with a particular emphasis on its potential as a target for anti-cancer drugs. Future research will further elucidate the specific mechanisms of action of TAOK kinase in different types of tumors and explore its clinical application prospects.

Harnessing potential COX-2 engagement for boosting anticancer activity of substituted 2-mercapto-4(3H)-quinazolinones with promising EGFR/VEGFR-2 inhibitory activities

We designed and synthesized new quinazolinone-tethered phenyl thiourea/thiadiazole derivatives 4-26. Based on their structural characteristics, these compounds were proposed to have a multi-target mode of action for their anticancer activities. Using the MTT assay method, antiproliferative effects were assessed against three human cancer cell lines (HEPG-2, MCF-7, and HCT-116). In vitro assessment for enzymatic inhibitory activity of the most active compounds 4, 9 and 20 was done for EGFR, VEGFR-2 and COX-2 as potential targets. The screened compounds showed low micromolar IC50 inhibitory effects against the three targets. Compound 9 demonstrated similar EGFR/VEGFR-2 inhibitory effect to the control drugs and potential inhibitory activity for COX-2 enzyme. In MCF-7 cells, the most active analog 9 caused 41.02% total apoptosis, and arrested the cell cycle at the G2/M phase. Taken as a whole, the findings of this study provide significant new understandings into the relationship between COX inhibition and cancer therapy. Furthermore, the outcomes showcased the encouraging efficacy of these compounds with a multi-target mechanism, making them excellent choices for additional research and development into possible anticancer drug.

Allosteric Changes in the Conformational Landscape of Src Kinase upon Substrate Binding

Precise regulation of protein kinase activity is crucial in cell functions, and its loss is implicated in various diseases. The kinase activity is regulated by interconverting active and inactive states in the conformational landscape. However, how protein kinases switch conformations in response to different signals such as the binding at distinct sites remains incompletely understood. Here, we predict the binding mode for the peptide substrate to Src tyrosine kinase using enhanced conformational sampling simulations (totaling 24 μs) and then investigate changes in the conformational landscape upon substrate binding by conducting unbiased molecular dynamics simulations (totaling 50 μs) initiated from the apo and substrate-bound forms. Unexpectedly, the peptide substrate binding significantly facilitates the transitions from active to inactive conformations in which the αC helix is directed outward, the regulatory spine is broken, and the ATP-binding domain is perturbed. We also explore an underlying residue-contact network responsible for the allosteric conformational changes. Our results are in accord with the recent experiments reporting the negative cooperativity between the peptide substrate and ATP binding to tyrosine kinases and will contribute to advancing our understanding of the regulation mechanisms for kinase activity.

Predicting binding events in very flexible, allosteric, multi-domain proteins

Knowledge of the structures formed by proteins and small molecules is key to understand the molecular principles of chemotherapy and for designing new and more effective drugs. During the early stage of a drug discovery program, it is customary to predict ligand-protein complexes in silico, particularly when screening large compound databases. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology to generate bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites by exploiting only information on the unbound structure and the putative binding sites. The protocol is validated on the paradigm enzyme adenylate kinase, for which we generated a significant fraction of bound-like structures. A fraction of these conformations, employed in ensemble-docking calculations, allowed to find native-like poses of substrates and inhibitors (binding to the active form of the enzyme), as well as catalytically incompetent analogs (binding the inactive form). Our protocol provides a general framework for the generation of bound-like conformations of challenging drug targets that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening, in the prediction of the impact of amino acid mutations on structure and dynamics, and in protein engineering.

Design, preparation and biological evaluation of new Rociletinib-inspired analogs as irreversible EGFR inhibitors to treat non-small-cell-lung cancer

Epidermal growth factor receptor (EGFR) kinase has been implicated in the uncontrolled cell growth associated with non-small cell lung cancer (NSCLC). This has prompted the development of 3 generations of EGFR inhibitors over the last 2 decades due to the rapid development of drug resistance issues caused by clinical mutations, including T790M, L858R and the double mutant T790M & L858R. In this work we report the design, preparation and biological assessment of new irreversible 2,4-diaminopyrimidine-based inhibitors of EGFR kinase. Twenty new compounds have been prepared and evaluated which incorporate a range of electrophilic moieties. These include acrylamide, 2-chloroacetamide and (2E)-3-phenylprop-2-enamide, to allow reaction with residue Cys797. In addition, more polar groups have been incorporated to provide a better balance of physical properties than clinical candidate Rociletinib. Inhibitory activities against EGFR wildtype (WT) and EGFR T790M & L858R have been evaluated along with cytotoxicity against EGFR-overexpressing (A549, A431) and normal cell lines (HepG2). Selectivity against JAK3 kinase as well as physicochemical properties determination (logD7.4 and phosphate buffer solubility) have been used to profile the compounds. We have identified 20, 21 and 23 as potent mutant EGFR inhibitors (≤20 nM), with comparable or better selectivity over WT EGFR, and lower activity at JAK3, than Osimertinib or Rociletinib. Compounds 21 displayed the best combination of EGFR mutant activity, JAK3 selectivity, cellular activity and physicochemical properties. Finally, kinetic studies on 21 were performed, confirming a covalent mechanism of action at EGFR.

The novel ROCK2 selective inhibitor NRL-1049 preserves the blood-brain barrier after acute injury

Endothelial blood-brain barrier (BBB) dysfunction is critical in the pathophysiology of brain injury. Rho-associated protein kinase (ROCK) activation disrupts BBB integrity in the injured brain. We aimed to test the efficacy of a novel ROCK2 inhibitor in preserving the BBB after acute brain injury. We characterized the molecular structure and pharmacodynamic and pharmacokinetic properties of a novel selective ROCK2 inhibitor, NRL-1049, and its first metabolite, 1-hydroxy-NRL-1049 (referred to as NRL-2017 hereon) and tested the efficacy of NRL-1049 on the BBB integrity in rodent models of acute brain injury. Our data show that NRL-1049 and NRL-2017 both inhibit ROCK activity and are 44-fold and 17-fold more selective towards ROCK2 than ROCK1, respectively. When tested in a mouse model of cortical cryoinjury, NRL-1049 significantly attenuated the increase in water content. Interestingly, 60% of the mice in the vehicle arm developed seizures within 2 hours after cryoinjury versus none in the NRL-1049 arm. In spontaneously hypertensive rats, NRL-1049 attenuated the dramatic surge in Evans Blue extravasation compared with the vehicle arm after transient middle cerebral artery occlusion. Hemorrhagic transformation was also reduced. We show that NRL-1049, a selective ROCK2 inhibitor, is a promising drug candidate to preserve the BBB after brain injury.

SVIL promotes ovarian cancer progression and epithelial-mesenchymal transition under hypoxic conditions through the TGF-β/Smad pathway

OBJECTIVE

Ovarian cancer is the malignant tumor with the highest mortality rate in gynecology. We aimed to identify novel genes that promote ovarian cancer progression and epithelial-mesenchymal transition under hypoxic conditions.

METHODS

We screened SVIL as a hypoxia-associated target in ovarian cancer and explored the related molecular mechanisms. We assessed the effects of SVIL on ovarian cancer progression and metastasis in clinical samples and cellular hypoxia models. Further, we investigated the relevant pathways of SVIL and confirmed the effects of SVIL on ovarian cancer progression by using nude mouse in situ tumor models.

RESULTS

We found that SVIL was significantly highly expressed in the hypoxic environment of ovarian cancer, and SVIL expression correlated with patient prognosis.CCK8, Wound-healing assay, Transwell assay, Western Blot, and apoptosis assays revealed that knockdown of SVIL inhibited the activation of the TGFβ1/smad2/3 pathway, which attenuated the progression and epithelial-mesenchymal transition(EMT) of ovarian cancer and alleviated cisplatin resistance by increasing cisplatin-induced apoptosis. Furthermore, in a nude mouse ovarian cancer in situ model, we found that the knockdown of SVIL significantly inhibited tumor growth and metastasis.

CONCLUSION

SVIL highly expressed in the hypoxic microenvironment can increase ovarian cancer progression and cisplatin resistance by activating TGFβ1/smad2/3 pathway. Our study demonstrated that SVIL may be a novel target for the treatment of ovarian cancer.

GPT4Kinase: High-accuracy prediction of inhibitor-kinase binding affinity utilizing large language model

The accurate prediction of inhibitor-kinase binding affinity is crucial in biological research and medical applications. Particularly, kinases play a pivotal role in numerous cellular processes and are essential enzymes in Mitogen-Activated Protein Kinase (MAPK) signaling pathway. This present study harnesses the capabilities of Large Language Models (LLMs), specifically GPT-4, to predict the binding affinity between inhibitors and kinases within the MAPK pathway, including Raf protein kinase (RAF), Mitogen-activated protein kinase kinase (MEK) and Extracellular Signal-Regulated Kinase (ERK). Remarkably, GPT-4 achieved an impressive 87.31 % accuracy in prediction on RAF binding affinity, and 77.00 % accuracy in comprehensive prediction tasks, substantially outperforming existing mainstream methods such as Autodock Vina (21.21 %), BatchDTA (52.00 %) and KIPP (59.60 %). Furthermore, GPT-4 was employed to delineate the features of high-affinity and low-affinity molecules, as well as their contributing functional groups. These contributing groups were subsequently validated through molecular docking. Additionally, to validate the generalizability of the method, we applied it to six other kinases and achieved a maximum accuracy of 83.78 %. Also, we utilized a dataset comprising over 200 kinases, obtaining a high accuracy of 66.20 %. The study showcases the transformative impact of LLMs on molecular binding affinity prediction, with major implications for biological sciences and therapeutic development.

Identification, biological evaluation, and crystallographic analysis of coumestrol as a novel dual-specificity tyrosine-phosphorylation-regulated kinase 1A inhibitor

Alzheimer's disease (AD) is an irreversible neurodegenerative disease, with tau pathology caused by abnormally activated dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) being one of the culprits. Coumestrol, a phytoestrogen and natural antioxidant found in various plants, has been reported to alleviate AD, but the underlying mechanism remains unclear. We confirmed coumestrol as a novel DYRK1A inhibitor through enzyme-based assays, X-ray crystallography, and cell line experiments. Coumestrol exhibited minimal cytotoxicity at concentrations up to 100 μM in cell types such as N2A and SH-SY5Y and reduced DYRK1A-induced phosphorylated tau protein levels by >50 % at 60 μM. In the tau protein phosphorylation and microtubule assembly assay, coumestrol at 30 μM reduced phosphorylated tau by >50 % and restored the microtubule assembly process. Coumestrol also significantly reduced amyloid-β (Aβ)-induced oxidative stress in microglia at 1 μM. In zebrafish larvae co-overexpressing DYRK1A and tau, coumestrol mitigated neuronal damage and protected motor function at 48 h-postfertilization. Our results suggest that coumestrol has potential therapeutic effects in AD by inhibiting DYRK1A, lowering p-Tau levels, restoring microtubule assembly, and protecting microglia cells from Aβ-induced cell death, providing new insights into the development of coumestrol as a potential AD treatment.

N-Benzyl piperidine Fragment in Drug Discovery

The N-benzyl piperidine (N-BP) structural motif is commonly employed in drug discovery due to its structural flexibility and three-dimensional nature. Medicinal chemists frequently utilize the N-BP motif as a versatile tool to fine-tune both efficacy and physicochemical properties in drug development. It provides crucial cation-π interactions with the target protein and also serves as a platform for optimizing stereochemical aspects of potency and toxicity. This motif is found in numerous approved drugs and clinical/preclinical candidates. This review focuses on the applications of the N-BP motif in drug discovery campaigns, emphasizing its role in imparting medicinally relevant properties. The review also provides an overview of approved drugs, the clinical and preclinical pipeline, and discusses its utility for specific therapeutic targets and indications, along with potential challenges.

Design and synthesis of novel Thiazolo[5,4-b]pyridine derivatives as potent and selective EGFR-TK inhibitors targeting resistance Mutations in non-small cell lung cancer

A novel series of substituted thiazolo[5,4-b]pyridine analogues were rationally designed and synthesized via a multi-step synthetic pathway, including Suzuki cross-coupling reaction. The anticancer activity of all forty-five synthesized derivatives was evaluated against HCC827, H1975, and A549 cancer cell lines utilizing the standard MTT assay. A significant number of the thiazolo[5,4-b]pyridine derivatives exhibited potent anticancer activity. Notably, compounds 10b, 10c, 10h, 10i, and 10k emerged as the most promising anticancer agents. The lead compound, N-(3-(6-(2-aminopyrimidin-5-yl)thiazolo[5,4-b]pyridin-2-yl)-2-methylphenyl)-2,5-difluorobenzenesulfonamide (10k), displayed remarkable potency with IC50 values of 0.010 μM, 0.08 μM, and 0.82 μM against the HCC827, NCI-H1975 and A-549 cancer cell lines, respectively, which were comparable to the clinically approved drug Osimertinib. Importantly, the potent derivatives 10b, 10c, 10h, 10i, and 10k exhibited selective cytotoxicity towards cancer cells and showing no toxicity against the normal BEAS-2B cell line at concentrations exceeding 35 μM. Mechanistic studies revealed that the active compound 10k acts as an EGFR-TK autophosphorylation inhibitor in HCC827 cells. Furthermore, apoptosis assays demonstrated that compound 10k induced substantial early apoptosis (31.9 %) and late apoptosis (8.8 %) in cancer cells, in contrast to the control condition exhibiting only 2.0 % early and 1.6 % late apoptosis. Molecular docking simulations of the synthesized compounds revealed that they formed essential hinge interactions and established hydrogen bonding with Cys797, indicating potential target engagement. These findings highlight the potential of the synthesized thiazolo [(Woodburn, 1999; Zigrossi et al., 2022) 5,45,4-b]pyridine derivatives as promising anticancer agents, warranting further investigation for the development of novel targeted therapies against non-small cell lung cancer.

A web portal for exploring kinase-substrate interactions

Interactions between protein kinases and their substrates are critical for the modulation of complex signaling pathways. Currently, there is a large amount of information available about kinases and their substrates in disparate public databases. However, these data are difficult to interpret in the context of cellular systems, which can be facilitated by examining interactions among multiple proteins at once, such as the network of interactions that constitute a signaling pathway. We present KiNet, a user-friendly web portal that integrates and shares information about kinase-substrate interactions from multiple databases of post-translational modifications. KiNet enables the visual exploration of these interactions in systems contexts, such as pathways, domain families, and custom protein set inputs, in an interactive fashion. We expect KiNet to be useful as a knowledge discovery tool for kinase-substrate interactions, and the aggregated KiNet dataset to be useful for protein kinase studies and systems-level analyses. The portal is available at https://kinet.kinametrix.com/ .

Discovery of small molecule inhibitors of neddylation catalyzing enzymes for anticancer therapy

Protein neddylation, a type of post-translational modifications, involves the transfer of the ubiquitin-like protein NEDD8 to the lysine residues of a target substrate, which is catalyzed by the NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). Cullin family proteins, core components of Cullin-RING E3 ubiquitin ligases (CRLs), are the most well-known physiological substrates of neddylation. CRLs, activated upon cullin neddylation, promote the ubiquitination of a variety of key signaling proteins for proteasome degradation, thereby regulating many critical biological functions. Abnormal activation of neddylation enzymes as well as CRLs has been frequently observed in various human cancers and is associated with poor prognosis for cancer patients. Consequently, targeting neddylation has emerged as a promising strategy for the development of novel anticancer therapeutics. This review first briefly introduces the properties of protein neddylation and its role in cancer, and then systematically summarizes all reported chemical inhibitors of the three neddylation enzymes, providing a focused, up to date, and comprehensive resource in the discovery and development of these small molecule inhibitors.

Development and assessment of novel pyrazole-thiadiazol hybrid derivatives as VEGFR-2 inhibitors: design, synthesis, anticancer activity evaluation, molecular docking, and molecular dynamics simulation

Cancer remains a significant health challenge globally, requiring the development of targeted chemotherapeutics capable of specifically inhibiting cancer cell growth. Angiogenesis is one of the key features of tumor growth and metastasis and is, therefore, an important target for the treatment of many tumors. The vascular endothelial growth factor (VEGF) signaling pathway has proven to be a promising lead in anticancer therapy due to the central role it plays in tumor angiogenesis. Vascular endothelial growth factor receptor-2 (VEGFR-2) is a key mediator in the signaling pathway regulating angiogenesis. Targeting VEGFR-2 may disrupt angiogenesis, leading to a reduction in tumor blood supply and tumor progression. The design, synthesis, and assessment of novel VEGFR-2 inhibitor derivatives are the focus of this study, with particular emphasis on incorporating the pyrazole-thiadiazol pharmacophore into the molecular structure. Taking advantage of the pharmacophoric properties of pyrazole and 1,3,4-thiadiazol, compounds with different substituents in the main structure were designed and synthesized. The compounds were also evaluated for antiproliferative activity against cancer cell lines. Compound 4e demonstrated the highest activity among all compounds, with an IC50 of 9.673 ± 0.399 μM against HT-29 cells and 23.081 ± 0.400 μM against NIH3T3 cells. To further support the inhibitory activity of compound 4e, an in silico study was performed. Compound 4e demonstrated strong binding to the active site of VEGFR-2 in molecular docking studies, forming hydrogen bonds with key amino acid residues. The stability of the compound in the enzyme's active site was demonstrated through molecular dynamics simulations.

A novel class of potent antiangiogenic and antioxidant pyrazoles: synthesis, bioactivity, docking and ADMET studies

Aim: Angiogenesis is the hallmark of cancer progression driven by VEGF/VEGFR-2 signalling pathway, inhibition of which could be a solution to tackle the progression of tumour cells and thus arresting their growth.Materials & methods: A novel class of pyrazoles was synthesized using arginine and dibromo ketones. Antiangiogenic activity was performed by in vivo yolk sac method. Antioxidant activity was evaluated by hydroxyl and superoxide radical scavenging assays. Docking studies were performed to determine the pyrazoles' binding potential with VEGFR-2 receptor and VEGF tyrosine kinase. ADMET properties were calculated using SwissADME and admetSAR for drug-likeness.Results: Compounds 5a-e showed significant antiangiogenic effects. Compound 5f exhibited effective hydroxyl and superoxide radical scavenging activities. Docking results confirmed the potential binding efficiency with VEGFR-2 receptor over VEGF tyrosine kinase, thus, functioning as competitive-inhibitors. ADMET studies revealed that the compounds possess favourable drug-like qualities.Conclusion: This study presents a novel class of pyrazoles as promising antioxidant and antiangiogenic agents with favourable drug-likeness properties.

Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation

Cyclin-dependent kinases (CDKs), including CDK12 and CDK13, play crucial roles in regulating the cell cycle and RNA polymerase II activity, making them vital targets for cancer therapies. SR4835 is a selective inhibitor of CDK12/13, showing significant potential for treating triple-negative breast cancer. To elucidate the selective mechanism of SR4835 among three CDKs (CDK13/12/9), we developed an innovative enhanced sampling method, integrated well-tempered metadynamics-umbrella sampling (IMUS). IMUS synergistically combines the comprehensive pathway exploration capability of well-tempered metadynamics (WT-MetaD) with the precise free energy calculation capability of umbrella sampling, enabling the efficient and accurate characterization of drug-target interactions. The accurate calculation of binding free energy and the detailed analysis of the kinetic mechanism of the drug-target interaction using IMUS successfully elucidate the drug selectivity mechanism targeting the three CDKs, showing that the selectivity is primarily arising from differences in the stability of H-bonds within the Hinge region of the kinases and the interaction patterns during the protein-ligand recognition process. These findings also underscore the utility of IMUS in efficiently and accurately capturing drug-target interaction processes with clear mechanisms.

GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity

The proteins within the human epidermal growth factor receptor (EGFR) family, members of the tyrosine kinase receptor family, play a pivotal role in the molecular mechanisms driving the development of various tumors. Tyrosine kinase inhibitors, key compounds in targeted therapy, encounter challenges in cancer treatment due to emerging drug resistance mutations. Consequently, machine learning has undergone significant evolution to address the challenges of cancer drug discovery related to EGFR family proteins. However, the application of deep learning in this area is hindered by inherent difficulties associated with small-scale data, particularly the risk of overfitting. Moreover, the design of a model architecture that facilitates learning through multi-task and transfer learning, coupled with appropriate molecular representation, poses substantial challenges. In this study, we introduce GraphEGFR, a deep learning regression model designed to enhance molecular representation and model architecture for predicting the bioactivity of inhibitors against both wild-type and mutant EGFR family proteins. GraphEGFR integrates a graph attention mechanism for molecular graphs with deep and convolutional neural networks for molecular fingerprints. We observed that GraphEGFR models employing multi-task and transfer learning strategies generally achieve predictive performance comparable to existing competitive methods. The integration of molecular graphs and fingerprints adeptly captures relationships between atoms and enables both global and local pattern recognition. We further validated potential multi-targeted inhibitors for wild-type and mutant HER1 kinases, exploring key amino acid residues through molecular dynamics simulations to understand molecular interactions. This predictive model offers a robust strategy that could significantly contribute to overcoming the challenges of developing deep learning models for drug discovery with limited data and exploring new frontiers in multi-targeted kinase drug discovery for EGFR family proteins.

Biological Evaluations and Computer-Aided Approaches of Janus Kinases 2 and 3 Inhibitors for Cancer Treatment: A Review

Cancer remains one of the leading diseases of mortality worldwide. Janus kinases 2/3 (JAK2/3) have been considered a drug target for the development of drugs to treat different types of cancer. JAK2/3 play a critical role in innate immunity, inflammation, and hematopoiesis by mediating the signaling of numerous cytokines, growth factors, and interferons. The current focus is to develop new selective inhibitors for each JAK type. In this review, the current strategies of computer-aided studies, and biological evaluations against JAK2/3 are addressed. We found that the new synthesized JAK2/3 inhibitors are prone to containing heterocyclic aromatic rings such as pyrimidine, pyridine, and pyrazolo [3,4-d]pyrimidine. Moreover, inhibitors of natural origin derived from plant extracts and insects have shown suitable inhibitory capacities. Computer-assisted studies have shown the important features of inhibitors for JAK2/3 binding. Biological evaluations showed that the inhibition of the JAK receptor affects its related signaling pathway. Although the reviewed compounds showed good inhibitory capacity in vitro and in vivo, more in-depth studies are needed to advance toward full approval of cancer treatments in humans.

FDA-approved small molecule kinase inhibitors for cancer treatment (2001-2015): Medical indication, structural optimization, and binding mode Part I

The dysregulation of kinases has emerged as a major class of targets for anticancer drug discovery given its node roles in the etiology of tumorigenesis, progression, invasion, and metastasis of malignancies, which is validated by the FDA approval of 28 small molecule kinase inhibitor (SMKI) drugs for cancer treatment at the end of 2015. While the preclinical and clinical data of these drugs are widely presented, it is highly essential to give an updated review on the medical indications, design principles and binding modes of these anti-tumor SMKIs approved by the FDA to offer insights for the future development of SMKIs with specific efficacy and safety.

Diverse functions of Tribbles homolog 3 in cancers and its potential as a therapeutic target

Currently, cancer is the second leading cause of death worldwide, and potential targeted drugs and molecular pathways for cancer development and progression have been a hot research topic worldwide. In recent years, the importance of the kinase superfamily in diseases has been well demonstrated by studies on various molecular mechanisms of kinases and the successful application of their inhibitors in diseases. Pseudokinases are members of the kinase superfamily, which have been increasingly documented to play a crucial role in cancers year after year. As a member of pseudokinases, tribbles homolog 3 (TRIB3) also exerts diverse functions in different cancers through different interacting proteins and molecular pathways, especially in tumor immunity, stemness, drug resistance, metabolism, and autophagy. In addition, peptide drugs targeting TRIB3 have high specificity in preclinical studies, which shows great promise for TRIB3 application in diseases including cancers. In this review, we dissect diverse functions played by TRIB3 in different cancers, describing the underlying mechanisms in detail. Notably, inhibitors and agonists currently available for TRIB3 are discussed, indicating the potential for TRIB3 as a therapeutic target.

Dual-targeted NAMPT inhibitors as a progressive strategy for cancer therapy

In mammals, nicotinamide phosphoribosyltransferase (NAMPT) is a crucial enzyme in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway catalyzing the condensation of nicotinamide (NAM) with 5-phosphoribosyl-1-pyrophosphate (PRPP) to produce nicotinamide mononucleotide (NMN). Given the pivotal role of NAD+ in a range of cellular functions, including DNA synthesis, redox reactions, cytokine generation, metabolism, and aging, NAMPT has become a promising target for many diseases, notably cancer. Therefore, various NAMPT inhibitors have been reported and classified as first and second-generation based on their chemical structures and design strategies, dual-targeted being one. However, most NAMPT inhibitors suffer from several limitations, such as dose-dependent toxicity and poor pharmacokinetic properties. Consequently, there is no clinically approved NAMPT inhibitor. Hence, research on discovering more effective and less toxic dual-targeted NAMPT inhibitors with desirable pharmacokinetic properties has drawn attention recently. This review summarizes the previously reported dual-targeted NAMPT inhibitors, focusing on their design strategies and advantages over the single-targeted therapies.

Targeted small molecule therapy and inhibitors for lymphoma

Lymphoma, a blood tumor, has become the ninth most common cancer in the world in 2020. Targeted inhibition is one of the important treatments for lymphoma. At present, there are many kinds of targeted drugs for the treatment of lymphoma. Studies have shown that Histone deacetylase, Bruton's tyrosine kinase and phosphoinositide 3-kinase all play an important role in the occurrence and development of tumors and become important and promising inhibitory targets. This article mainly expounds the important role of these target protein in tumors, and introduces the mechanism of action, structure-activity relationship and clinical research of listed small molecule inhibitors of these targets, hoping to provide new ideas for the treatment of lymphoma.