AIMC Topic: Enzyme Inhibitors

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Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.

Journal of computer-aided molecular design Jan 8, 2020
Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secret...
Ligands Enzyme Inhibitors Neural Networks, Computer Amyloid Precursor Protein Secretases Molecular Docking Simulation Drug Design Aspartic Acid Endopeptidases Protein Binding Macrocyclic Compounds Humans Binding Sites
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Endocannabinoid degradation inhibitors ameliorate neuronal and synaptic alterations following traumatic brain injury.

Journal of neurophysiology Jan 8, 2020
Our previous work showed that lateral fluid percussion injury to the sensorimotor cortex (SMC) of anesthetized rats increased neuronal synaptic hyperexcitability in layer 5 (L5) neurons in ex vivo brain slices 10 days postinjury. Furthermore, endocan...
Piperidines Enzyme Inhibitors Carbamates Amidohydrolases Rats, Wistar Machine Learning Rats Animals Brain Injuries, Traumatic Male Piperazines Succinimides Excitatory Postsynaptic Potentials Endocannabinoids Benzamides Benzodioxoles Sensorimotor Cortex Pyramidal Cells Monoacylglycerol Lipases Electrophysiological Phenomena
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Deep learning enables rapid identification of potent DDR1 kinase inhibitors.

Nature biotechnology Sep 2, 2019
We have developed a deep generative model, generative tensorial reinforcement learning (GENTRL), for de novo small-molecule design. GENTRL optimizes synthetic feasibility, novelty, and biological activity. We used GENTRL to discover potent inhibitors...
Humans Models, Molecular Molecular Structure Dogs Drug Evaluation, Preclinical Microsomes, Liver Animals Deep Learning Mice Rats Enzyme Inhibitors Protein Conformation Discoidin Domain Receptor 1
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Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors.

Journal of chemical information and modeling Jul 19, 2019
Molecular dynamics simulations provide valuable insights into the behavior of molecular systems. Extending the recent trend of using machine learning techniques to predict physicochemical properties from molecular dynamics data, we propose to conside...
Molecular Dynamics Simulation Enzyme Inhibitors Tankyrases Deep Learning Time Factors Computational Biology
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SAR study on inhibitors of GIIA secreted phospholipase A using machine learning methods.

Chemical biology & drug design Feb 4, 2019
GIIA secreted phospholipase A (GIIA sPLA ) is a potent target for drug discovery. To distinguish the activity level of the inhibitors of GIIA sPLA , we built 24 classification models by three machine learning algorithms including support vector machi...
Group II Phospholipases A2 Humans Machine Learning Cluster Analysis Structure-Activity Relationship Principal Component Analysis Enzyme Inhibitors
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Application of molecular docking and PSO-SVR intelligent approaches in antimalarial activity prediction of enantiomeric cycloguanil analogues.

SAR and QSAR in environmental research Nov 1, 2018
A series of antifolate compounds, i.e. 1-(4-chlorophenyl)-6,6-dimethyl-1,3,5-triazine-2,4-diamine, or cycloguanil analogues, have shown effective inhibiting properties against Plasmodium falciparum dihydrofolate reductase (PfDHFR). In this work, the ...
Proguanil Tetrahydrofolate Dehydrogenase Stereoisomerism Folic Acid Antagonists Substrate Specificity Triazines Molecular Structure Antimalarials Enzyme Inhibitors Quantitative Structure-Activity Relationship Machine Learning Molecular Docking Simulation Protein Binding Plasmodium falciparum Algorithms Reproducibility of Results
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Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase.

International microbiology : the official journal of the Spanish Society for Microbiology Aug 24, 2018
Shikimate dehydrogenase (HpSDH) (EC 1.1.1.25) is a key enzyme in the shikimate pathway of Helicobacter pylori (H. pylori), which catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. Targeting HpSDH has been recognize...
Alcohol Oxidoreductases Crystallography, X-Ray Protein Conformation Helicobacter pylori Anti-Bacterial Agents Drug Evaluation, Preclinical Molecular Docking Simulation Enzyme Inhibitors Microbial Sensitivity Tests Catalytic Domain Computational Biology
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Amino acid conjugated antimicrobial drugs: Synthesis, lipophilicity- activity relationship, antibacterial and urease inhibition activity.

European journal of medicinal chemistry Dec 29, 2017
Present work describes the in vitro antibacterial evaluation of some new amino acid conjugated antimicrobial drugs. Structural modification was attempted on the three existing antimicrobial pharmaceuticals namely trimethoprim, metronidazole, isoniazi...
Metronidazole Pseudomonas aeruginosa Salmonella typhi Hydrophobic and Hydrophilic Interactions Microbial Sensitivity Tests Anti-Bacterial Agents Enzyme Inhibitors Structure-Activity Relationship Escherichia coli Bacillus Staphylococcus aureus Molecular Structure Isoniazid Amino Acids Dose-Response Relationship, Drug Trimethoprim Urease
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From word models to executable models of signaling networks using automated assembly.

Molecular systems biology Nov 24, 2017
Word models (natural language descriptions of molecular mechanisms) are a common currency in spoken and written communication in biomedicine but are of limited use in predicting the behavior of complex biological networks. We present an approach to b...
Neural Networks, Computer Computer Simulation Language Melanoma Cell Line, Tumor Gene Expression Regulation, Neoplastic Models, Genetic Skin Neoplasms Antineoplastic Agents Humans Proto-Oncogene Proteins p21(ras) Proto-Oncogene Proteins B-raf Vemurafenib Indoles Enzyme Inhibitors Drug Resistance, Neoplasm Signal Transduction Tumor Suppressor Protein p53 Natural Language Processing DNA Damage Sulfonamides
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Commercial glucometer as signal transducer for simple evaluation of DNA methyltransferase activity and inhibitors screening.

Analytica chimica acta Nov 23, 2017
DNA methyltransferase (MTase) plays an important role in many biological processes and has been recognized as a predictive cancer biomarker far before other signs of malignancy and a therapeutic target in cancer treatment. Thus simple and sensitive d...
Humans Antineoplastic Agents Biosensing Techniques Signal Transduction DNA Methylation Enzyme Inhibitors Enzyme Assays DNA-Cytosine Methylases Limit of Detection Equipment Design Drug Evaluation, Preclinical Blood Glucose Self-Monitoring
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