AIMC Topic: Catalytic Domain

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Atomic Ga Site Enables Photonanozymes with Specific Inhibition Modes for Primary Drug Screening.

Analytical chemistry Jun 10, 2025
Enzyme inhibition plays a crucial role in drug discovery by governing interactions between molecules and distinct enzymatic sites, facilitating the identification of early drug candidates. However, most nanozymes have been limited to single active si...
Catalytic Domain Nitriles Antithyroid Agents Humans Drug Evaluation, Preclinical Enzyme Inhibitors
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Substrate Activation Efficiency in Active Sites of Hydrolases Determined by QM/MM Molecular Dynamics and Neural Networks.

International journal of molecular sciences May 26, 2025
The active sites of enzymes are able to activate substrates and perform chemical reactions that cannot occur in solutions. We focus on the hydrolysis reactions catalyzed by enzymes and initiated by the nucleophilic attack of the substrate's carbonyl ...
Catalytic Domain Hydrolases Molecular Dynamics Simulation Quantum Theory Hydrolysis Neural Networks, Computer Substrate Specificity
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Design, synthesis, and evaluation of triazolo[1,5-a]pyridines as novel and potent α‑glucosidase inhibitors.

Scientific reports May 22, 2025
α-Glucosidase is a key enzyme responsible for controlling the blood glucose, making a pivotal target in the treatment of type 2 diabetes mellitus. Present work introducestriazolo[1,5-a]pyridine as a novel, potent scaffold for α-glucosidase inhibition...
Humans Molecular Docking Simulation Triazoles Catalytic Domain alpha-Glucosidases Drug Design Pyridines Structure-Activity Relationship Glycoside Hydrolase Inhibitors
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Evolutionary Dynamics and Functional Differences in Clinically Relevant Pen β-Lactamases from spp.

Journal of chemical information and modeling May 2, 2025
Antimicrobial resistance (AMR) is a global threat, with species contributing significantly to difficult-to-treat infections. The Pen family of β-lactamases are produced by all spp., and their mutation or overproduction leads to the resistance of β-...
Markov Chains Catalytic Domain Burkholderia Molecular Dynamics Simulation beta-Lactamases Evolution, Molecular Mutation
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Machine Learning-Guided Screening and Molecular Docking for Proposing Naturally Derived Drug Candidates Against MERS-CoV 3CL Protease.

International journal of molecular sciences Mar 26, 2025
In this study, we utilized machine learning techniques to identify potential inhibitors of the MERS-CoV 3CL protease. Among the models evaluated, the Random Forest (RF) algorithm exhibited the highest predictive performance, achieving an accuracy of ...
Protease Inhibitors Coronavirus 3C Proteases Catalytic Domain Middle East Respiratory Syndrome Coronavirus Humans Machine Learning Molecular Docking Simulation Drug Discovery Antiviral Agents Molecular Dynamics Simulation
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Geometry-encoded molecular dynamics enables deep learning insights into P450 regiospecificity control.

Scientific reports Mar 3, 2025
Cytochrome P450 1A2, as many isoenzymes, can generate multiple metabolites from a single substrate. A loose coupling between substrate binding and oxygen activation makes possible substrate reorientations at the active site prior to catalysis. In the...
Cytochrome P-450 CYP1A2 Caffeine Substrate Specificity Deep Learning Oxidation-Reduction Oxygen Molecular Dynamics Simulation Catalytic Domain Humans
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Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.

Journal of chemical information and modeling Feb 10, 2025
Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes reve...
Machine Learning Models, Molecular Quantum Theory Serine Proteases Static Electricity Biocatalysis Protein Engineering Catalytic Domain
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Correlating enzymatic reactivity for different substrates using transferable data-driven collective variables.

Proceedings of the National Academy of Sciences of the United States of America Nov 26, 2024
Machine learning (ML) is transforming the investigation of complex biological processes. In enzymatic catalysis, one significant challenge is identifying the reactive conformations (RC) of the enzyme:substrate complex where the substrate assumes a pr...
Substrate Specificity Pancreatic alpha-Amylases Oligosaccharides Catalytic Domain Protein Conformation Humans Machine Learning
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Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.

Nature communications Aug 27, 2024
Annotating active sites in enzymes is crucial for advancing multiple fields including drug discovery, disease research, enzyme engineering, and synthetic biology. Despite the development of numerous automated annotation algorithms, a significant trad...
Algorithms Catalytic Domain Molecular Sequence Annotation Enzymes Deep Learning Computational Biology Databases, Protein
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Machine learning-based QSAR and LB-PaCS-MD guided design of SARS-CoV-2 main protease inhibitors.

Bioorganic & medicinal chemistry letters Jun 24, 2024
The global outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 virus had led to profound respiratory health implications. This study focused on designing organoselenium-based inhibitors targeting the SARS-CoV-2 main protease (M). The ligand-bi...
Protease Inhibitors Coronavirus 3C Proteases Isoindoles Organoselenium Compounds Antiviral Agents Azoles Molecular Dynamics Simulation Catalytic Domain Quantitative Structure-Activity Relationship COVID-19 SARS-CoV-2 Drug Design Humans Machine Learning
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