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Structure-Based Virtual Screening Identifies 2-Arylthiazole-4-Carboxylic Acids as a Novel Class of Nanomolar Affinity Ligands for the CaMKIIα Hub Domain.
J Med Chem
January 2025
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
The Ca/calmodulin-dependent protein kinase II α (CaMKIIα) plays a crucial role in regulating neuronal signaling and higher brain functions, being involved in various brain diseases. Utilization of small molecules targeting the CaMKIIα hub domain has proved to be a promising strategy for specific CaMKIIα modulation and future therapy. Through an structure-based virtual screening campaign, we herein identified 2-arylthiazole-4-carboxylic acids as a new class of high-affinity CaMKIIα hub ligands.
View Article and Find Full Text PDFDO-GMA: An End-to-End Drug-Target Interaction Identification Framework with a Depthwise Overparameterized Convolutional Network and the Gated Multihead Attention Mechanism.
J Chem Inf Model
January 2025
Geneis (Beijing) Co. Ltd., Beijing 100102, China.
Identification of potential drug-target interactions (DTIs) is a crucial step in drug discovery and repurposing. Although deep learning effectively deciphers DTIs, most deep learning-based methods represent drug features from only a single perspective. Moreover, the fusion method of drug and protein features needs further refinement.
View Article and Find Full Text PDFDirected Evolution's Selective Use of Quantum Tunneling in Designed Enzymes─A Combined Theoretical and Experimental Study.
J Phys Chem B
January 2025
Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States.
Natural enzymes are powerful catalysts, reducing the apparent activation energy for reactions and enabling chemistry to proceed as much as 10 times faster than the corresponding solution reaction. It has been suggested for some time that, in some cases, quantum tunneling can contribute to this rate enhancement by offering pathways through a barrier inaccessible to activated events. A central question of interest to both physical chemists and biochemists is the extent to which evolution introduces mechanisms below the barrier, or tunneling mechanisms.
View Article and Find Full Text PDFStrategic Mutations in Designer Native Peptides Combat NLRP3 Inflammasome Activation in Neurodegenerative Disorders.
J Med Chem
January 2025
Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka, India.
Nucleotide-binding oligomerization domain (NOD)-, leucine-rich repeat (LRR)-, and pyrin domain (PYD)-containing protein 3 (NLRP3) form an inflammasome by assembling with apoptosis-associated speck-like protein containing a CARD (ASC) and procaspase-1 that plays a pivotal role in various neurodegenerative diseases such as Alzheimer's and Parkinson diseases. We designed native peptides derived from the PYDs of NLRP3 and ASC based on their interfacial interaction to inhibit NLRP3 inflammasome formation. Screening revealed that , derived from NLRP3, inhibits inflammasome activation.
View Article and Find Full Text PDFChemoproteomic Profiling of Clickable Fumarate Probes for Target Identification and Mechanism of Action Studies.
ACS Chem Biol
January 2025
Biogen, Chemical Biology & Proteomics, 225 Binney Street, Cambridge, Massachusetts 02142, United States.
Dimethyl fumarate (DMF) is an established oral therapy for multiple sclerosis worldwide. Although the clinical efficacy of these fumarate esters has been extensively investigated, the mode of action and pharmacokinetics of fumarates have not been fully elucidated due to their broad-spectrum reactivity and complex metabolism in vivo. To better understand the mechanism of action of DMF and its active metabolite, monomethyl fumarate (MMF), we designed and utilized clickable probes to visualize and enrich probe-modified proteins.
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