AIMC Topic: Protease Inhibitors

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Fingerprint-Based Machine Learning for SARS-CoV-2 and MERS-CoV Inhibition: Highlighting the Potential of Bayesian Neural Networks.

Journal of chemical information and modeling Dec 10, 2025
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two important targets in current drug discovery, mainly due to the COVID-19 pandemic and the MERS-CoV outbreaks in recent yea...
Humans Neural Networks, Computer Machine Learning Bayes Theorem Middle East Respiratory Syndrome Coronavirus Protease Inhibitors Coronavirus 3C Proteases SARS-CoV-2 Drug Discovery Antiviral Agents
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Design of Carbon Nanotube Inhibitors for Main Proteinase of SARS-CoV-2: A Combined Deep Learning and Molecular Dynamics Simulation Study.

The journal of physical chemistry. B Nov 10, 2025
The rapid development of machine learning (ML) and deep learning (DL) methods provides new opportunities for innovative drug discovery. While these techniques are widely used in docking organic molecules (drugs) with protein, an evaluation of the per...
Coronavirus 3C Proteases Nanotubes, Carbon Binding Sites Protease Inhibitors Humans Deep Learning SARS-CoV-2 Molecular Dynamics Simulation Molecular Docking Simulation Drug Design
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Integrating Physics-Based Simulations with Data-Driven Deep Learning Represents a Robust Strategy for Developing Inhibitors Targeting the Main Protease.

Journal of chemical information and modeling Aug 6, 2025
The coronavirus main protease, essential for viral replication, is a well-validated antiviral target. Here, we present Deep-CovBoost, a computational pipeline integrating deep learning with free energy perturbation (FEP) simulations to guide the stru...
Drug Design Deep Learning Antiviral Agents Molecular Dynamics Simulation Humans SARS-CoV-2 Thermodynamics Protease Inhibitors Coronavirus 3C Proteases
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Ionic liquids and lysosomotropic detergents as inhibitors of the SARS-CoV-2 main protease: QSAR modeling, synthesis and biological testing.

Biochemical and biophysical research communications Jun 28, 2025
SARS-CoV-2 infection is highly contagious, prompting the World Health Organization to classify it as a global public health emergency. The virus has numerous potential hosts, which complicates efforts for effective prevention, diagnosis, and treatmen...
Humans Machine Learning COVID-19 SARS-CoV-2 Detergents Quantitative Structure-Activity Relationship Antiviral Agents Protease Inhibitors Ionic Liquids Coronavirus 3C Proteases COVID-19 Drug Treatment
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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...
Cysteine Proteinase Inhibitors Drug Discovery Antiviral Agents Molecular Dynamics Simulation Coronavirus 3C Proteases Coronavirus Papain-Like Proteases COVID-19 Drug Treatment Protease Inhibitors COVID-19 SARS-CoV-2 Molecular Docking Simulation Humans Machine Learning
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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...
Coronavirus 3C Proteases COVID-19 SARS-CoV-2 Antiviral Agents Drug Resistance, Viral Humans Protease Inhibitors Machine Learning Mutation Molecular Dynamics Simulation
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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 Antiviral Agents Molecular Docking Simulation Machine Learning Molecular Dynamics Simulation Drug Discovery Catalytic Domain
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Enhancing HCV NS3 Inhibitor Classification with Optimized Molecular Fingerprints Using Random Forest.

International journal of molecular sciences Mar 17, 2025
The classification of Hepatitis C virus (HCV) NS3 inhibitors is essential for identifying potential antiviral agents through computational methods. This study aims to develop an optimized machine learning (ML) model using random forest (RF) and molec...
Humans Machine Learning Drug Discovery Hepacivirus Serine Endopeptidases Antiviral Agents Random Forest Viral Proteases Viral Nonstructural Proteins Nucleoside-Triphosphatase Protease Inhibitors DEAD-box RNA Helicases
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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...
Deep Learning Structure-Activity Relationship Antiviral Agents SARS-CoV-2 Protease Inhibitors Molecular Docking Simulation Pyrazoles Combinatorial Chemistry Techniques Humans Drug Design 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...
COVID-19 Drug Treatment Molecular Docking Simulation Coronavirus Papain-Like Proteases Small Molecule Libraries High-Throughput Screening Assays Drug Discovery Humans Coronavirus 3C Proteases Protease Inhibitors Antiviral Agents Machine Learning SARS-CoV-2
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