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Learning from nature has emerged as a promising strategy for catalyst development, wherein the remarkable performance of catalysts selected by nature over billions of years of evolution serves as a basis for the creative design of high-performance catalysts. Hydrogenases, with their exceptional catalytic activity in hydrogen oxidation and production, have been employed as prototypes for human learning to achieve better catalyst design. A comprehensive understanding of hydrogenases' structures and catalytic mechanisms is crucial to replicate and exceed their performance. Computational modeling has proven to be a powerful tool for elucidating the reduction chemistry of [FeFe]-hydrogenases. This review overviews recent computational and experimental efforts, focusing on density functional theory (DFT) calculations applied to [FeFe] hydrogenases. It summarizes current knowledge on identifying active sites in [FeFe] hydrogenases and the reaction cycles involved in hydrogen metabolism.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140359 | PMC |
http://dx.doi.org/10.1002/advs.202408297 | DOI Listing |
Front Immunol
September 2025
Department of Thoracic Surgery, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; The Second Clinical Medical College, Jinan University), Shenzhen, Guangdong, China.
Background: Lung cancer remains the leading cause of cancer-related mortality globally, primarily due to late-stage diagnosis, molecular heterogeneity, and therapy resistance. Key biomarkers such as EGFR, ALK, KRAS, and PD-1 have revolutionized precision oncology; however, comprehensive structural and clinical validation of these targets is crucial to enhance therapeutic efficacy.
Methods: Protein sequences for EGFR, ALK, KRAS, and PD-1 were retrieved from UniProt and modeled using SWISS-MODEL to generate high-confidence 3D structures.
Mater Today Bio
October 2025
Leibniz Institute of Polymer Research Dresden, Division Polymer Biomaterials Science, Max Bergmann Center of Biomaterials Dresden, 01069, Dresden, Germany.
Glycosaminoglycan-based biohybrid hydrogels represent a powerful class of cell-instructive materials with proven potential in tissue engineering and regenerative medicine. Their biomedical functionality relies on a nanoscale polymer network that standard microscopy techniques cannot resolve. Here, we introduce an advanced analytical approach that integrates transmission electron microscopy, X-ray scattering, and computer simulations to directly and quantitatively characterize the nanoscale molecular network structure of these hydrogels.
View Article and Find Full Text PDFChem Biol Drug Des
September 2025
School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa.
Molecular hybridization of isoniazid with hydrophobic aromatic moieties represents a promising strategy for the development of novel anti-tubercular therapeutics. In this study, a series of hybrid molecules (5a-i) was synthesized by linking isoniazid with aromatic sulfonate esters via a hydrazone bridge. Molecular docking studies revealed that these compounds interact effectively with the catalytic triad of the InhA enzyme (Y158, F149, and K165), suggesting their potential as InhA inhibitors.
View Article and Find Full Text PDFSAR QSAR Environ Res
August 2025
Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao, China.
Phosphorylation plays an important role in the activity of CDK2 and inhibitor binding, but the corresponding molecular mechanism is still insufficiently known. To address this gap, the current study innovatively integrates molecular dynamics (MD) simulations, deep learning (DL) techniques, and free energy landscape (FEL) analysis to systematically explore the action mechanisms of two inhibitors (SCH and CYC) when CDK2 is in a phosphorylated state and bound state of CyclinE. With the help of MD trajectory-based DL, key functional domains such as the loops L3 loop and L7 are successfully identified.
View Article and Find Full Text PDFSAR QSAR Environ Res
August 2025
Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India.
, a causative agent of lymphatic filariasis, relies on its endosymbiont for survival. MurE ligase, a key enzyme in peptidoglycan biosynthesis, serves as a promising drug target for anti-filarial therapy. In this study, we employed a hierarchical virtual screening pipeline to identify phytochemical inhibitors targeting the MurE enzyme of the endosymbiont of (MurE).
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