X-ray crystallography is a powerful technique for studying protein-ligand interactions. Advances in techniques have meant that it is now possible to routinely determine the structures of ligand complexes in the majority of cases where crystallization conditions and protein structures are already known. Ligand soaking or cocrystallization, together with the potential use of molecular replacement, provides data for determining the structures of a protein in complex with ligands. Furthermore, advances in protein structure model building facilitate automatic ligand fitting to residual electron density in the protein-ligand complex.
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http://dx.doi.org/10.1007/978-1-62703-398-5_17 | DOI Listing |
J Chem Theory Comput
January 2025
State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
Molecular docking is a crucial technique for elucidating protein-ligand interactions. Machine learning-based docking methods offer promising advantages over traditional approaches, with significant potential for further development. However, many current machine learning-based methods face challenges in ensuring the physical plausibility of generated docking poses.
View Article and Find Full Text PDFPharmaceuticals (Basel)
December 2024
Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana.
: Pteridine reductase 1 (PTR1) has been one of the prime targets for discovering novel antileishmanial therapeutics in the fight against Leishmaniasis. This enzyme catalyzes the NADPH-dependent reduction of pterins to their tetrahydro forms. While chemotherapy remains the primary treatment, its effectiveness is constrained by drug resistance, unfavorable side effects, and substantial associated costs.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil.
The COVID-19 pandemic has caused over 7 million deaths globally in the past four years. spp. (Siparunaceae), which is used in Brazilian folk medicine, is considered a genus with potential antiviral alternatives.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and School of Life Sciences, Yunnan University, Kunming 650091, China.
The human transmembrane protease, serine 2 (TMPRSS2), essential for SARS-CoV-2 entry, is a key antiviral target. Here, we computationally profiled the TMPRSS2-binding affinities of 15 antiviral compounds. Molecular dynamics (MD) simulations for the docked complexes revealed that three compounds exited the substrate-binding cavity (SBC), suggesting noncompetitive inhibition.
View Article and Find Full Text PDFSci Rep
January 2025
Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
This study investigates the interrelationship between human telomerase reverse transcriptase (hTERT) and ferroptosis in precursor-B (pre-B) acute lymphoblastic leukemia (ALL), specifically examining how hTERT modulation affects ferroptotic cell death pathways. Given that hTERT overexpression characterizes various cancer phenotypes and elevated telomerase activity is observed in early-stage and relapsed ALL, we investigated the molecular mechanisms linking hTERT regulation and ferroptosis in leukemia cells. The experimental design employed Nalm-6 and REH cell lines under three distinct conditions: curcumin treatment, hTERT siRNA knockdown, and their combination.
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