An overview of issues associated with the design and development of low molecular weight inhibitors of protein-protein interactions is presented. Areas discussed include information on the nature of protein-protein interfaces, methods to characterize those interfaces and methods by which that information is applied towards ligand identification and design. Specific examples of the strategy for the identification of inhibitors of protein-protein interactions involving the proteins p56lck kinase, ERK2 and the calcium-binding protein S100B are presented. Physical characterization of the inhibitors identified in those studies shows them to have drug-like and lead-like properties, indicating their potential to be developed into therapeutic agents.
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J Chem Inf Model
January 2025
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
Predicting protein-protein interactions (PPIs) is crucial for advancing drug discovery. Despite the proposal of numerous advanced computational methods, these approaches often suffer from poor usability for biologists and lack generalization. In this study, we designed a deep learning model based on a coattention mechanism that was capable of both PPI and site prediction and used this model as the foundation for PPI-CoAttNet, a user-friendly, multifunctional web server for PPI prediction.
View Article and Find Full Text PDFJ Med Chem
January 2025
Chemical Biology Section, Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States.
Autophagy, a recycling process in eukaryotes, contributes to tumor growth and metastasis by alleviating cellular stress and facilitating survival and chemoresistance. The development of small molecules that selectively inhibit this pathway has proven challenging and is required to determine if autophagy inhibition can be harnessed as an effective therapeutic strategy in cancer. Compound 19 was previously identified as a selective autophagy inhibitor that targets the ATG14L-Beclin1 protein-protein interaction, which regulates the formation, localization, and function of VPS34 Complex I to initiate autophagy.
View Article and Find Full Text PDFBiochemistry
January 2025
Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg 405 30, Sweden.
The apoptosome, a critical protein complex in apoptosis regulation, relies on intricate interactions between its components, particularly the proteins containing the Caspase Activation and Recruitment Domain (CARD). This work presents a thorough computational analysis of the stability and specificity of CARD-CARD interactions within the apoptosome. Departing from available crystal structures, we identify important residues for the interaction between the CARD domains of Apaf-1 and Caspase-9.
View Article and Find Full Text PDFMetab Brain Dis
January 2025
Xuzhou Engineering Research Center of Medical Genetics and Transformation, Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
The widely used Radix Astragali (RA) has significant therapeutic effects on cognitive impairment (CI) caused by type 2 diabetes (T2DM). However, the effective active ingredients and the precise mechanism underly RA alleviation of T2DM-induced CI still require further study. In this study, we aim to elucidate whether and how jaranol, a key effective active ingredient in RA, influences CI in db/db mice.
View Article and Find Full Text PDFPrev Nutr Food Sci
December 2024
School of Food Science & Biotechnology, Kyungpook National University, Daegu 41566, Korea.
, a medicinal plant traditionally used in Southeast Asia, exerts protective effects against various inflammatory diseases, primarily due to its rich alkaloid content. Despite substantial evidence supporting its anti-inflammatory properties, the biological activities of are unclear. This study aimed to elucidate anticolitis mechanisms of alkaloids (CFAs) using an integrative approach of network pharmacology and molecular docking analyses.
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