We introduce a versatile metal-organic framework (MOF) for encapsulation and immobilization of various guests using highly ordered internal water network. The unique water-mediated entrapment mechanism is applied for structural elucidation of 14 bioactive compounds, including 3 natural product intermediates whose 3D structures are clarified. The single-crystal X-ray diffraction analysis reveals that incorporated guests are surrounded by hydrogen-bonded water networks inside the pores, which uniquely adapt to each molecule, providing clearly defined crystallographic sites. The calculations of host-solvent-guest structures show that the guests are primarily interacting with the MOF through weak dispersion forces. In contrast, the coordination and hydrogen bonds contribute less to the total stabilization energy, however, they provide highly directional point interactions, which help align the guests inside the pore.
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http://dx.doi.org/10.1038/s41467-023-44401-w | DOI Listing |
J Chem Inf Model
January 2025
Department of Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.
Machine learning (ML) models now play a crucial role in predicting properties essential to drug development, such as a drug's logscale acid-dissociation constant (p). Despite recent architectural advances, these models often generalize poorly to novel compounds due to a scarcity of ground-truth data. Further, these models lack interpretability.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
Host defense antimicrobial peptides (AMPs) are promising lead molecules with which to develop antibiotics against drug-resistant bacterial pathogens. Thanatin, an inducible antimicrobial peptide involved in the host defense of insects, is gaining considerable attention in the generation of novel classes of antibiotics. Thanatin or thanatin-based analog peptides are extremely potent in killing bacterial pathogens in the Enterobacteriaceae family, including drug-resistant strains of and .
View Article and Find Full Text PDFNature
January 2025
Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, USA.
Proximity ferroelectricity is an interface-associated phenomenon in electric-field-driven polarization reversal in a non-ferroelectric polar material induced by one or more adjacent ferroelectric materials. Here we report proximity ferroelectricity in wurtzite ferroelectric heterostructures. In the present case, the non-ferroelectric layers are AlN and ZnO, whereas the ferroelectric layers are AlBN, AlScN and ZnMgO.
View Article and Find Full Text PDFBiomolecules
November 2024
Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
The nucleocapsid (N) protein is one of the four structural proteins in SARS-CoV-2, playing key roles in viral assembly, immune evasion, and stability. One of its primary functions is to protect viral RNA by forming the nucleocapsid. However, the precise mechanisms by which the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear.
View Article and Find Full Text PDFbioRxiv
December 2024
Simons Machine Learning Center, New York Structural Biology Center, New York, United States.
It is now possible to generate large volumes of high-quality images of biomolecules at near-atomic resolution and in near-native states using cryogenic electron microscopy/electron tomography (Cryo-EM/ET). However, the precise annotation of structures like filaments and membranes remains a major barrier towards applying these methods in high-throughput. To address this, we present TARDIS (ransformer-bsed apid imensionless nstance egmentation), a machine-learning framework for fast and accurate annotation of micrographs and tomograms.
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