An unnatural amino acid was synthesized to incorporate a quinone methide-generating activity-based probe for protein tyrosine phosphatases (PTPs) and then integrated into a PTP1B-specific substrate. The resulting probe led to preferential labeling of PTP1B in cell lysates in the presence of PTP4A3.
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http://dx.doi.org/10.1016/j.bmcl.2009.04.081 | DOI Listing |
J Phys Chem B
January 2025
Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States.
Macrocyclization or stapling is an important strategy for increasing the conformational stability and target-binding affinity of peptides and proteins, especially in therapeutic contexts. Atomistic simulations of such stapled peptides and proteins could help rationalize existing experimental data and provide predictive tools for the design of new stapled peptides and proteins. Standard approaches exist for incorporating nonstandard amino acids and functional groups into the force fields required for MD simulations and have been used in the context of stapling for more than a decade.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, Texas 78712, United States.
Language modeling applied to biological data has significantly advanced the prediction of membrane penetration for small-molecule drugs and natural peptides. However, accurately predicting membrane diffusion for peptides with pharmacologically relevant modifications remains a substantial challenge. Here, we introduce PeptideCLM, a peptide-focused chemical language model capable of encoding peptides with chemical modifications, unnatural or noncanonical amino acids, and cyclizations.
View Article and Find Full Text PDFThe 26S proteasome complex is the hub for regulated protein degradation in the cell. It is composed of two biochemically distinct complexes: the 20S core particle with proteolytic active sites in an internal chamber and the 19S regulatory particle, consisting of a lid and base subcomplex. The base contains ubiquitin receptors and an AAA+ (ATPases associated with various cellular activities) motor that unfolds substrates prior to degradation.
View Article and Find Full Text PDFOrg Lett
January 2025
Organic Chemistry Department, Faculty of Science, Autonomous University of Madrid, 28049 Madrid, Spain.
The functionalization of the C-N bond of amines is a straightforward strategy for the construction of complex scaffolds or for the late-stage functionalization of pharmaceuticals. Herein, we describe a photoredox-catalyzed strategy for the deaminative alkylation of primary amine-derived isonitriles that provides unnatural amino acid derivatives under mild conditions. The use of silacarboxylic acids as silyl radical precursors enables the generation of carbon-centered radicals that allow the construction of Csp-Csp bonds via a Giese-type addition, avoiding the undesired hydrodeamination product.
View Article and Find Full Text PDFBioorg Med Chem
December 2024
Department of Immunology and Microbiology, Scripps Research, United States; Department of Chemistry, Scripps Research, United States. Electronic address:
The emergence of antibiotic-resistant bacteria has intensified the need for novel therapeutic strategies targeting bacterial virulence rather than growth or survival. Bacterial virulence involves complex processes that enable pathogens to invade and survive within host cells. Chemical biology has become a powerful tool for dissecting these virulence mechanisms at the molecular level.
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