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MSA clustering enhances AF-Multimer's ability to predict conformational landscapes of protein-protein interactions.
Bioinform Adv
December 2024
Laboratory of Experimental Biophysics, Center for Advanced Technologies, Tashkent, 100174, Uzbekistan.
Motivation: Understanding the conformational landscape of protein-ligand interactions is critical for elucidating the binding mechanisms that govern these interactions. Traditional methods like molecular dynamics (MD) simulations are computationally intensive, leading to a demand for more efficient approaches. This study explores how multiple sequence alignment (MSA) clustering enhance AF-Multimer's ability to predict conformational landscapes, particularly for proteins with multiple conformational states.
View Article and Find Full Text PDFLigand docking in the sigma-1 receptor compared to the sigma-1 receptor-BiP complex and the effects of agonists and antagonists on C. elegans lifespans.
Biomed Pharmacother
December 2024
Center of Excellence on Natural Products for Neuroprotection and Anti-Ageing, Chulalongkorn University, Bangkok 10330, Thailand; Research, Innovation and International Affairs, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand. Electronic address:
Model organisms are commonly used to study human diseases; we set out to understand the relevance of several model organisms with relation to the σ1R protein. The study explored the interactions of σ1R with various agonists, antagonists across different species. Ligand and protein-protein (σ1R-BiP) docking approaches were used to understand the significance of σ1R in modulating neuroprotective mechanisms and its potential role in Alzheimer's.
View Article and Find Full Text PDFKouqiangjie formula alleviates diabetic periodontitis by regulating alveolar bone homeostasis via miR-29a-3p-mediated Dkk-1/Wnt/β-catenin signaling pathway.
J Ethnopharmacol
December 2024
Department of Radiology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China. Electronic address:
Ethnopharmacological Relevance: Diabetic periodontitis (DP) is a commonly co-occurring complication in diabetes patients characterized by advanced gum disease and bone resorption. Conventional treatment modalities often fail to adequately address the underlying biological disruptions caused by diabetes. The use of traditional medicinal formulas Kouqiangjie Formula (KQJF) potentially offers novel therapeutic approaches for DP, but its detailed regulatory mechanisms remain unclear.
View Article and Find Full Text PDFWD repeat domain 5 (WDR5) inhibitors: a patent review (2016-present).
Expert Opin Ther Pat
January 2025
Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
Introduction: WDR5 is an epigenetic scaffolding protein that has attracted significant interest as an anti-cancer drug target, especially in MLL-rearranged leukemias. The most druggable 'WIN-site' on WDR5, which tethers WDR5 to chromatin, has been successfully targeted with multiple classes of exquisitely potent small-molecule protein-protein interaction inhibitors. Earlier progress has also been made on the development of WDR5 degraders and inhibitors at the 'WBM-site' on the opposite face of WDR5.
View Article and Find Full Text PDFTargeting Yes-Associated Protein (YAP) in Breast Cancer: In Silico Molecular Dynamics, Luminescence-Based In Vitro, and In Vivo Validation of Rauvolfia tetraphylla-Derived Inhibitors.
Luminescence
December 2024
Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia.
The study aims to elucidate the pharmacological mechanism of Rauvolfia tetraphylla against breast cancer through a comprehensive, multi-faceted approach. This includes molecular docking, molecular dynamics, and experimental validation. Initial screening via ADME analysis and network pharmacology identified key compounds and potential targets.
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