AIMC Topic: Coronavirus 3C Proteases

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Discovery of SARS-CoV-2 papain-like protease inhibitors through machine learning and molecular simulation approaches.

Drug discoveries & therapeutics Jun 27, 2025
The papain-like protease (PLpro), a cysteine protease found in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), plays a crucial role in viral replication by cleaving the viral polyproteins and interfering with the host's innate immune re...
Humans Molecular Dynamics Simulation COVID-19 Drug Treatment Protease Inhibitors Cysteine Proteinase Inhibitors Coronavirus 3C Proteases Coronavirus Papain-Like Proteases Machine Learning Molecular Docking Simulation COVID-19 Drug Discovery SARS-CoV-2 Antiviral Agents
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In-silico study of approved drugs as potential inhibitors against 3CLpro and other viral proteins of CoVID-19.

PloS one Jun 25, 2025
The global pandemic, due to the emergence of COVID-19, has created a public health crisis. It has a huge morbidity rate that was never comprehended in the recent decades. Despite numerous efforts, potent antiviral drugs are lacking. Repurposing of dr...
Computer Simulation SARS-CoV-2 Molecular Docking Simulation Antiviral Agents Humans Machine Learning COVID-19 COVID-19 Drug Treatment Coronavirus 3C Proteases Coronavirus Nucleocapsid Proteins Protein Binding Spike Glycoprotein, Coronavirus Drug Repositioning
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Enhancing the understandings on SARS-CoV-2 main protease (M) mutants from molecular dynamics and machine learning.

International journal of biological macromolecules Apr 10, 2025
While star drugs like Paxlovid have shown remarkable performance in combating SARS-CoV-2, we still face serious challenges such as viral mutants and resistance. In this study, we employ a computational framework combining molecular dynamics (MD) simu...
SARS-CoV-2 Antiviral Agents Mutation Humans Protease Inhibitors Machine Learning Coronavirus 3C Proteases COVID-19 Molecular Dynamics Simulation Drug Resistance, Viral
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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 ...
Middle East Respiratory Syndrome Coronavirus Protease Inhibitors Coronavirus 3C Proteases Humans Machine Learning Molecular Dynamics Simulation Molecular Docking Simulation Drug Discovery Catalytic Domain Antiviral Agents
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Rational design and synthesis of pyrazole derivatives as potential SARS-CoV-2 M inhibitors: An integrated approach merging combinatorial chemistry, molecular docking, and deep learning.

Bioorganic & medicinal chemistry Feb 3, 2025
The global impact of SARS-CoV-2 has highlighted the urgent need for novel antiviral therapies. This study integrates combinatorial chemistry, molecular docking, and deep learning to design, evaluate and synthesize new pyrazole derivatives as potentia...
Molecular Docking Simulation Drug Design Humans SARS-CoV-2 Pyrazoles Deep Learning Protease Inhibitors Antiviral Agents Combinatorial Chemistry Techniques Structure-Activity Relationship Coronavirus 3C Proteases
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Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors.

Journal of chemical information and modeling Jan 16, 2025
The global impact of SARS-CoV-2 highlights the need for treatments beyond vaccination, given the limited availability of effective medications. While Pfizer introduced , an FDA-approved antiviral targeting the SARS-CoV-2 main protease (Mpro), this st...
Small Molecule Libraries Coronavirus 3C Proteases Coronavirus Papain-Like Proteases COVID-19 Drug Treatment High-Throughput Screening Assays Protease Inhibitors Humans Molecular Docking Simulation Machine Learning Drug Discovery SARS-CoV-2 Antiviral Agents
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F-CPI: A Multimodal Deep Learning Approach for Predicting Compound Bioactivity Changes Induced by Fluorine Substitution.

Journal of medicinal chemistry Dec 20, 2024
Fluorine (F) substitution is a common method of drug discovery and development. However, there are no accurate approaches available for predicting the bioactivity changes after F-substitution, as the effect of substitution on the interactions between...
Humans SARS-CoV-2 Drug Discovery Coronavirus 3C Proteases Deep Learning Antiviral Agents Fluorine
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Generative adversarial network (GAN) model-based design of potent SARS-CoV-2 M inhibitors using the electron density of ligands and 3D binding pockets: insights from molecular docking, dynamics simulation, and MM-GBSA analysis.

Molecular diversity Nov 30, 2024
Deep learning-based generative adversarial network (GAN) frameworks have recently been developed to expedite the drug discovery process. These models generate novel molecules from scratch and validate them through molecular docking simulation to iden...
Drug Design Deep Learning Antiviral Agents Protein Binding COVID-19 SARS-CoV-2 Molecular Docking Simulation Humans Binding Sites Coronavirus 3C Proteases Molecular Dynamics Simulation Protease Inhibitors Generative Adversarial Networks Ligands COVID-19 Drug Treatment
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TDFFM: Transformer and Deep Forest Fusion Model for Predicting Coronavirus 3C-Like Protease Cleavage Sites.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2024
COVID-19, caused by the highly contagious SARS-CoV-2 virus, is distinguished by its positive-sense, single-stranded RNA genome. A thorough understanding of SARS-CoV-2 pathogenesis is crucial for halting its proliferation. Notably, the 3C-like proteas...
Computational Biology Humans Decision Trees COVID-19 SARS-CoV-2 Coronavirus 3C Proteases Algorithms Deep Learning
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Generative artificial intelligence performs rudimentary structural biology modeling.

Scientific reports Aug 21, 2024
Natural language-based generative artificial intelligence (AI) has become increasingly prevalent in scientific research. Intriguingly, capabilities of generative pre-trained transformer (GPT) language models beyond the scope of natural language tasks...
Protein Conformation Coronavirus 3C Proteases SARS-CoV-2 Models, Molecular Humans Amino Acids Artificial Intelligence COVID-19
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