In the absence of an experimentally determined binding mode for the cyclopentapeptide CXCR4 antagonists, we have rationally designed conformationally constrained analogues to further probe the small peptide binding pocket of CXCR4. Two different rigidification strategies were employed, both resulting in highly potent ligands (9 and 13). The information provided by this cyclopentapeptide ligand series will be very valuable in the development of novel peptidomimetic CXCR4 antagonists.
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http://dx.doi.org/10.1021/jm300926y | DOI Listing |
J Chem Theory Comput
January 2025
Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark.
The minimal basis iterative Stockholder (MBIS) decomposition of molecular electron densities into atomic quantities is an attractive approach for deriving electrostatic parameters in force fields. The MBIS-derived atomic charges, however, in general tend to overestimate the molecular dipole and quadrupole moments by ∼10%. We show that it is possible to derive a constrained MBIS model where the atomic charges or a combination of atomic charges and dipoles exactly reproduce the molecular dipole and quadrupole moments for molecules.
View Article and Find Full Text PDFRSC Chem Biol
January 2025
School of Chemistry, Advanced Research Centre, University of Glasgow 11 Chapel Lane Glasgow G11 6EW UK
Peptide stapling is an effective strategy to stabilise α-helical peptides, enhancing their bioactive conformation and improving physiochemical properties. In this study, we apply our novel diyne-girder stapling approach to the MDM2/MDMX α-helical binding region of the p53 transactivation domain. By incorporation of an unnatural amino acid to create an optimal , + 7 bridge length, we developed a highly α-helical stapled peptide, 4, confirmed circular dichroism.
View Article and Find Full Text PDFTetrahedron Lett
March 2024
Department of Chemistry, University of California, Berkeley, CA 94720, United States.
In this manuscript, an oxidative carbon-carbon bond forming reaction to construct the framework of alkaloids such as scholarinine A is explored using a constrained substrate. Instead of the desired carbon-carbon bond formation between an indole C3 position and a malonate group, a competing carbon-nitrogen bond between the malonate and indole C3 position was observed to form. This work adds to the growing body of substrates for oxidative carbon-carbon bond formation and importantly, demonstrates that these reactions are challenging for some conformationally constrained substrates.
View Article and Find Full Text PDFNature
December 2024
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
Non-ribosomal peptide synthetases are assembly line biosynthetic pathways that are used to produce critical therapeutic drugs and are typically arranged as large multi-domain proteins called megasynthetases. They synthesize polypeptides using peptidyl carrier proteins that shuttle each amino acid through modular loading, modification and elongation steps, and remain challenging to structurally characterize, owing in part to the inherent dynamics of their multi-domain and multi-modular architectures. Here we have developed site-selective crosslinking probes to conformationally constrain and resolve the interactions between carrier proteins and their partner enzymatic domains.
View Article and Find Full Text PDFBiochem Biophys Res Commun
December 2024
Department of Biological Chemistry, Graduate School of Science, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan. Electronic address:
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