AIMC Topic: Pharmacophore

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Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles.

Journal of computer-aided molecular design Sep 26, 2025
Kinase profiling is an essential step in both hit identification and selectivity evaluation. Since in vitro testing of large chemical libraries is costly and time-consuming, a computational approach can be applied to narrow down the reasonable chemic...
Humans Neural Networks, Computer Machine Learning Protein Kinase Inhibitors Small Molecule Libraries Pharmacophore Graph Neural Networks Drug Design Drug Discovery Models, Molecular
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Retrospective Benchmarking and Novel Shape-Pharmacophore Based Implementation of the MORLD Method for the Autonomous Optimization of 3-Aroyl-1,4-diarylpyrroles (ARDAP).

Journal of chemical information and modeling Aug 5, 2025
The use of artificial intelligence (AI) is increasingly integral to the drug-discovery process, and among AI-driven methodologies, deep generative models stand out as one of the most promising approaches for hit identification and optimization. Here,...
Tubulin Modulators Tubulin Pyrroles Pharmacophore Algorithms Drug Discovery Benchmarking Retrospective Studies Molecular Docking Simulation
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Design and Synthesis of Magnolol Derivatives Using Integrated CNNs and Pharmacophore Approaches for Enhanced Parasiticidal Activity in Aquaculture.

Journal of agricultural and food chemistry Apr 16, 2025
Aquaculture is a rapidly growing sector of global food production, playing a vital role in poverty alleviation, food security, and income generation. However, it faces substantial challenges, particularly due to infections caused by the protozoan , l...
Drug Design Aquaculture Fish Diseases Structure-Activity Relationship Neural Networks, Computer Animals Ciliophora Infections Pharmacophore Dinoflagellida Molecular Structure Zebrafish Antiprotozoal Agents Biphenyl Compounds Goldfish Lignans
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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...
Molecular Dynamics Simulation Ligands Protein Kinase Inhibitors Phosphoinositide-3 Kinase Inhibitors Drug Discovery Protein Binding Phosphatidylinositol 3-Kinases Pharmacophore Machine Learning Molecular Docking Simulation Humans
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In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes.

Journal of computer-aided molecular design Dec 31, 2024
Diabetes represents a significant global health challenge associated with substantial healthcare costs and therapeutic complexities. Current diabetes therapies often entail adverse effects, necessitating the exploration of novel agents. Glucokinase (...
Glucokinase Enzyme Activators Molecular Docking Simulation Drug Design Diabetes Mellitus, Type 2 Humans Phenylalanine Hypoglycemic Agents Machine Learning Molecular Dynamics Simulation Computer Simulation Pharmacophore Peptides
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PharmRL: pharmacophore elucidation with deep geometric reinforcement learning.

BMC biology Dec 31, 2024
BACKGROUND: Molecular interactions between proteins and their ligands are important for drug design. A pharmacophore consists of favorable molecular interactions in a protein binding site and can be utilized for virtual screening. Pharmacophores are ...
Proteins Ligands Binding Sites Pharmacophore Algorithms Drug Design Deep Learning Humans
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Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies.

Molecular diversity Aug 16, 2024
Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibi...
Machine Learning Molecular Docking Simulation Protein Binding Mycobacterium tuberculosis Enzyme Inhibitors Antitubercular Agents Molecular Dynamics Simulation Protein Kinase Inhibitors Nucleoside-Phosphate Kinase Pharmacophore
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E-pharmacophore and deep learning based high throughput virtual screening for identification of CDPK1 inhibitors of Cryptosporidium parvum.

Computational biology and chemistry Aug 13, 2024
Cryptosporidiosis, a prevalent gastrointestinal illness worldwide, is caused by the protozoan parasite Cryptosporidium parvum. Calcium-dependent protein kinase 1 (CpCDPK1), crucial for the parasite's life cycle, serves as a promising drug target due ...
Molecular Docking Simulation Protein Kinase Inhibitors Deep Learning Molecular Structure Cryptosporidium parvum Protein Kinases Drug Evaluation, Preclinical Pharmacophore High-Throughput Screening Assays Antiprotozoal Agents
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Application of molecular dynamics-based pharmacophore and machine learning approaches to identify novel Mcl1 inhibitors through drug repurposing and mechanics research.

Physical chemistry chemical physics : PCCP Jun 6, 2024
Myeloid cell leukemia 1 (Mcl1), a critical protein that regulates apoptosis, has been considered as a promising target for antitumor drugs. The conventional pharmacophore screening approach has limitations in conformation sampling and data mining. He...
Quantum Theory Fluvastatin Myeloid Cell Leukemia Sequence 1 Protein Pharmacophore Cell Line, Tumor Humans Drug Repositioning Machine Learning Molecular Dynamics Simulation Antineoplastic Agents
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Unveiling G-protein coupled receptor kinase-5 inhibitors for chronic degenerative diseases: Multilayered prioritization employing explainable machine learning-driven multi-class QSAR, ligand-based pharmacophore and free energy-inspired molecular simulation.

International journal of biological macromolecules Apr 30, 2024
GRK5 holds a pivotal role in cellular signaling pathways, with its overexpression in cardiomyocytes, neuronal cells, and tumor cells strongly associated with various chronic degenerative diseases, which highlights the urgent need for potential inhibi...
Ligands Quantitative Structure-Activity Relationship Machine Learning Thermodynamics Protein Binding Protein Kinase Inhibitors Molecular Docking Simulation Chronic Disease Pharmacophore Humans Binding Sites Molecular Dynamics Simulation G-Protein-Coupled Receptor Kinase 5
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