AIMC Topic: Enzyme Inhibitors

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Study on SHP2 Conformational Transition and Structural Characterization of Its High-Potency Allosteric Inhibitors by Molecular Dynamics Simulations Combined with Machine Learning.

Molecules (Basel, Switzerland) Dec 24, 2024
The src-homology 2 domain-containing phosphatase 2 (SHP2) is a human cytoplasmic protein tyrosine phosphatase that plays a crucial role in cellular signal transduction. Aberrant activation and mutations of SHP2 are associated with tumor growth and im...
Machine Learning Protein Binding Molecular Dynamics Simulation Humans Protein Tyrosine Phosphatase, Non-Receptor Type 11 Enzyme Inhibitors Protein Conformation Allosteric Regulation
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Enhanced prediction of beta-secretase inhibitory compounds with mol2vec technique and machine learning algorithms.

SAR and QSAR in environmental research Dec 20, 2024
A comprehensive computational strategy that combined QSAR modelling, molecular docking, and ADMET analysis was used to discover potential inhibitors for β-secretase 1 (BACE-1). A dataset of 1,138 compounds with established BACE-1 inhibitory activitie...
Machine Learning Algorithms Enzyme Inhibitors Molecular Docking Simulation Amyloid Precursor Protein Secretases Molecular Dynamics Simulation Quantitative Structure-Activity Relationship
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Integrated machine learning and physics-based methods assisted de novo design of Fatty Acyl-CoA synthase inhibitors.

Expert opinion on drug discovery Nov 25, 2024
BACKGROUND: Tuberculosis is an infectious disease that has become endemic worldwide. The causative bacteria (Mtb) is targeted via several exciting drug targets. One newly discovered target is the Fatty Acyl-CoA synthase, which plays a significant ro...
Coenzyme A Ligases Drug Design Antitubercular Agents Lipid Metabolism Tuberculosis Mycobacterium tuberculosis Enzyme Inhibitors Machine Learning Humans Algorithms Molecular Docking Simulation
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Machine learning models to identify lead compound and substitution optimization to have derived energetics and conformational stability through docking and MD simulations for sphingosine kinase 1.

Molecular diversity Oct 17, 2024
Sphingosine kinases (SphKs) are a group of important enzymes that circulate at low micromolar concentrations in mammals and have received considerable attention due to the roles they play in a broad array of biological processes including apoptosis, ...
Humans Machine Learning Hydrogen Bonding Thermodynamics Phosphotransferases (Alcohol Group Acceptor) Molecular Docking Simulation Molecular Dynamics Simulation Enzyme Inhibitors
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Integration of 3D-QSAR, molecular docking, and machine learning techniques for rational design of nicotinamide-based SIRT2 inhibitors.

Computational biology and chemistry Oct 10, 2024
Selective inhibitors of sirtuin-2 (SIRT2) are increasingly recognized as potential therapeutics for cancer and neurodegenerative diseases. Derivatives of 5-((3-amidobenzyl)oxy)nicotinamides have been identified as some of the most potent and selectiv...
Niacinamide Humans Sirtuin 2 Machine Learning Drug Design Quantitative Structure-Activity Relationship Molecular Docking Simulation Molecular Structure Enzyme Inhibitors
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Recursive dynamics of GspE through machine learning enabled identification of inhibitors.

Computational biology and chemistry Sep 28, 2024
Type II secretion System has been increasingly recognized as a key driver of virulence in many pathogenic bacteria including Achromobacter xylosoxidans. ATPase GspE is the powerhouse of the T2SS. It powers the entire secretion process by binding with...
Anti-Bacterial Agents Molecular Docking Simulation Microbial Sensitivity Tests Molecular Structure Machine Learning Adenosine Triphosphatases Molecular Dynamics Simulation Enzyme Inhibitors
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Development of a machine learning-based target-specific scoring function for structure-based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors.

Journal of computational chemistry Sep 26, 2024
Human dihydroorotate dehydrogenase (hDHODH) is a flavin mononucleotide-dependent enzyme that can limit de novo pyrimidine synthesis, making it a therapeutic target for diseases such as autoimmune disorders and cancer. In this study, using the docking...
Oxidoreductases Acting on CH-CH Group Donors Molecular Structure Machine Learning Humans Molecular Dynamics Simulation Molecular Docking Simulation Ligands Enzyme Inhibitors Protein Binding Binding Sites Dihydroorotate Dehydrogenase
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Novel molecular inhibitor design for Plasmodium falciparum Lactate dehydrogenase enzyme using machine learning generated library of diverse compounds.

Molecular diversity Aug 20, 2024
Generative machine learning models offer a novel strategy for chemogenomics and de novo drug design, allowing researchers to streamline their exploration of the chemical space and concentrate on specific regions of interest. In cases with limited inh...
Plasmodium falciparum L-Lactate Dehydrogenase Machine Learning Antimalarials Small Molecule Libraries Drug Design Enzyme Inhibitors
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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...
Enzyme Inhibitors Protein Kinase Inhibitors Nucleoside-Phosphate Kinase Machine Learning Molecular Dynamics Simulation Molecular Docking Simulation Mycobacterium tuberculosis Protein Binding Pharmacophore Antitubercular Agents
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Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning.

Food chemistry Aug 3, 2024
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins thr...
Binding Sites Xanthine Oxidase Enzyme Inhibitors Peptides Quantitative Structure-Activity Relationship Molecular Docking Simulation Swine Machine Learning Animals
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