AIMC Topic: Protein Kinase Inhibitors

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Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?

Journal of chemical information and modeling Apr 1, 2025
Allosteric compounds offer an alternative mode of inhibition to orthosteric compounds with opportunities for selectivity and noncompetition. Structure-based drug design (SBDD) of allosteric compounds introduces complications compared to their orthost...
Deep Learning Ligands Protein Conformation Protein Kinase Inhibitors Molecular Docking Simulation Drug Design Cyclin-Dependent Kinase 2 Allosteric Regulation
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Discovery and characterization of novel FAK inhibitors for breast cancer therapy via hybrid virtual screening, biological evaluation and molecular dynamics simulations.

Bioorganic chemistry Mar 26, 2025
Focal adhesion kinase (FAK) is a critical drug target implicated in various disease pathways, including hematological malignancies and breast cancer. Therefore, identifying FAK inhibitors with novel scaffolds could offer new opportunities for develop...
Focal Adhesion Protein-Tyrosine Kinases Antineoplastic Agents Drug Evaluation, Preclinical Cell Proliferation Female Drug Screening Assays, Antitumor Humans Protein Kinase Inhibitors Dose-Response Relationship, Drug Breast Neoplasms Structure-Activity Relationship Focal Adhesion Kinase 1 Molecular Docking Simulation Molecular Structure Drug Discovery Molecular Dynamics Simulation
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Cyclin-Dependent Kinase 6 Deep Learning Protein Binding Phosphorylation Molecular Dynamics Simulation Protein Conformation Protein Kinase Inhibitors Humans Thermodynamics
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Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping.

Journal of biomedical informatics Mar 21, 2025
OBJECTIVE: To illustrate the use of an ontology in evaluating data quality in the medical field, focusing on phenotyping lung cancers.
Data Accuracy Biological Ontologies Humans ErbB Receptors Protein Kinase Inhibitors Phenotype Data Warehousing Lung Neoplasms Anaplastic Lymphoma Kinase Mutation
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Artificial intelligence system for predicting hand-foot skin reaction induced by vascular endothelial growth factor receptor inhibitors.

Scientific reports Mar 21, 2025
Hand-foot skin reaction (HFSR) is a common adverse effect of vascular endothelial growth factor receptor (VEGFR) inhibitors that significantly impacts patients' quality of life. Prevention and management of HFSR require individualized approaches, but...
Humans Aged Adult Protein Kinase Inhibitors Male Artificial Intelligence Receptors, Vascular Endothelial Growth Factor Middle Aged Female Hand-Foot Syndrome Risk Factors
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Integrated AI and machine learning pipeline identifies novel WEE1 kinase inhibitors for targeted cancer therapy.

Molecular diversity Mar 19, 2025
The dysregulation of the cell cycle in cancer underscores the therapeutic potential of targeting WEE1 kinase, a key regulator of the G2/M checkpoint. This study harnessed artificial intelligence (AI)-driven methodologies, particularly the MORLD platf...
Humans Artificial Intelligence Machine Learning Molecular Dynamics Simulation Molecular Targeted Therapy Protein Kinase Inhibitors Cell Cycle Proteins Neoplasms Molecular Docking Simulation Antineoplastic Agents Protein-Tyrosine Kinases
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Computational discovery of novel PI3KC2α inhibitors using structure-based pharmacophore modeling, machine learning and molecular dynamic simulation.

Journal of molecular graphics & modelling Mar 15, 2025
PI3KC2α is a lipid kinase associated with cancer metastasis and thrombosis. In this study, we present a novel computational workflow integrating structure-based pharmacophore modeling, machine learning (ML), and molecular dynamics (MD) simulations to...
Protein Kinase Inhibitors Phosphoinositide-3 Kinase Inhibitors Pharmacophore Phosphatidylinositol 3-Kinases Molecular Dynamics Simulation Humans Ligands Machine Learning Molecular Docking Simulation Drug Discovery Protein Binding
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Identification of Novel Fourth-Generation Allosteric Inhibitors Targeting Inactive State of EGFR T790M/L858R/C797S and T790M/L858R Mutations: A Combined Machine Learning and Molecular Dynamics Approach.

The journal of physical chemistry. B Mar 7, 2025
Targeted therapy with an allosteric inhibitor (AIs) is an important area of research in patients with epidermal growth factor receptor (EGFR) mutations. Current treatment of nonsmall cell lung cancer patients with EGFR mutations using orthosteric inh...
Mutation Molecular Dynamics Simulation Quantitative Structure-Activity Relationship ErbB Receptors Humans Machine Learning Protein Kinase Inhibitors Allosteric Regulation
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Using prognostic signatures and machine learning to identify core features associated with response to CDK4/6 inhibitor-based therapy in metastatic breast cancer.

Oncogene Feb 26, 2025
CDK4/6 inhibitors in combination with endocrine therapy are widely used to treat HR+/HER2- metastatic breast cancer leading to improved progression-free survival (PFS) compared to single agent endocrine therapy. Over 300 patients receiving standard-o...
Middle Aged Neoplasm Metastasis Female Humans Protein Kinase Inhibitors Gene Expression Regulation, Neoplastic Aged Cyclin-Dependent Kinase 4 Machine Learning Adult Progression-Free Survival Cyclin-Dependent Kinase 6 Prognosis Breast Neoplasms
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A deep-learning model for predicting tyrosine kinase inhibitor response from histology in gastrointestinal stromal tumor.

The Journal of pathology Feb 14, 2025
Over 90% of gastrointestinal stromal tumors (GISTs) harbor mutations in KIT or PDGFRA that can predict response to tyrosine kinase inhibitor (TKI) therapies, as recommended by NCCN (National Comprehensive Cancer Network) guidelines. However, gene seq...
Male Middle Aged Proto-Oncogene Proteins c-kit Deep Learning Tyrosine Kinase Inhibitors Pyrazoles Humans Treatment Outcome Mutation Receptor, Platelet-Derived Growth Factor alpha Protein Kinase Inhibitors Female Gastrointestinal Neoplasms Aged Pyrroles Gastrointestinal Stromal Tumors Triazines Imatinib Mesylate
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