AIMC Topic: Molecular Dynamics Simulation
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Deep learning-based dipeptidyl peptidase IV inhibitor screening, experimental validation, and GaMD/LiGaMD analysis.
BMC biology
Jul 1, 2025
BACKGROUND: Dipeptidyl peptidase-4 (DPP4) is considered a crucial enzyme in type 2 diabetes (T2D) treatment, targeted by inhibitors due to its role in cleaving glucagon-like peptide-1 (GLP-1). In this study, a novel DPP4 inhibitor screening strategy ...
Integrative machine learning and molecular simulation approaches identify GSK3β inhibitors for neurodegenerative disease therapy.
Scientific reports
Jul 1, 2025
Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD) and Parkinson's disease (PD), are a growing global health concern, especially among the elderly, posing significant challenges to well-being and survival. GSK3β, a serine/threonine...
Molecular dynamics-driven drug discovery.
Physical chemistry chemical physics : PCCP
Jun 18, 2025
Molecular dynamics (MD) simulation is an important tool and has a wide range of applications in many scientific fields, including drug discovery. Herein, focusing on drug discovery, the early compound discovery stage in particular, we discuss some of...
Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases.
Journal of the American Chemical Society
Jun 17, 2025
The translocation of DNA in polymerase (Pol) enzymes is a critical step for Pol-mediated nucleic acid polymerization, essential for storing and transmitting genetic information in all living organisms. During this process, the newly elongated double-...
Next-generation cancer therapeutics: unveiling the potential of liposome-based nanoparticles through bioinformatics.
Mikrochimica acta
Jun 16, 2025
Cancer remains one of the most deadly diseases in the world, requiring constant growth and improvements in therapeutic strategies. Traditional cancer treatments, such as chemotherapy, radiotherapy, and surgery, have limitations like off-target releas...
Engineered multi-domain lipid nanoparticles for targeted delivery.
Chemical Society reviews
Jun 16, 2025
Engineered lipid nanoparticles (LNPs) represent a breakthrough in targeted drug delivery, enabling precise spatiotemporal control essential to treat complex diseases such as cancer and genetic disorders. However, the complexity of the delivery proces...
Enzymatic carbon-fluorine bond cleavage by human gut microbes.
Proceedings of the National Academy of Sciences of the United States of America
Jun 13, 2025
Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated co...
Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation.
Journal of chemical information and modeling
Jun 6, 2025
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and postreaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that automates the gener...
Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments.
Journal of chemical information and modeling
Jun 5, 2025
Small-molecule drugs play a critical role in cancer therapy by selectively targeting key signaling pathways that drive tumor growth. While deep learning models have advanced drug discovery, there remains a lack of generative frameworks for covalent ...
Melting Profile of DNA in Crowded Solution: Model-Based Study.
International journal of molecular sciences
May 31, 2025
Recent advances in molecular dynamics (MD) simulations and the introduction of artificial intelligence (AI) have resulted in a significant increase in accuracy for structure prediction. However, the cell is a highly crowded environment consisting of ...
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