As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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http://dx.doi.org/10.1016/bs.pmch.2023.10.003 | DOI Listing |
J Chem Phys
January 2025
Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
The Effective Fragment Potential (EFP) method, a polarizable quantum mechanics-based force field for describing non-covalent interactions, is utilized to calculate protein-ligand interactions in seven inactive cyclin-dependent kinase 2-ligand complexes, employing structural data from molecular dynamics simulations to assess dynamic and solvent effects. Our results reveal high correlations between experimental binding affinities and EFP interaction energies across all the structural data considered. Using representative structures found by clustering analysis and excluding water molecules yields the highest correlation (R2 of 0.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Department of Chemistry, University of Washington, Seattle, Washington 98185, USA.
We derive a new expression for the strength of a hydrogen bond (VHB) in terms of the elongation of the covalent bond of the donor fragment participating in the hydrogen bond (ΔrHB) and the intermolecular coordinates R (separation between the heavy atoms) and θ (deviation of the hydrogen bond from linearity). The expression includes components describing the covalent D-H bond of the hydrogen bond donor via a Morse potential, the Pauli repulsion, and electrostatic interactions between the constituent fragments using a linear expansion of their dipole moment and a quadratic expansion of their polarizability tensor. We fitted the parameters of the model using ab initio electronic structure results for six hydrogen bonded dimers, namely, NH3-NH3, H2O-H2O, HF-HF, H2O-NH3, HF-H2O, and HF-NH3, and validated its performance for extended parts of their potential energy surfaces, resulting in a mean absolute error ranging from 0.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Research Institute of Chemistry, Peoples' Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia.
In this study, we report the first example of acyclic (amino)(N-pyridinium)carbenoid gold(III) complexes synthesized via a coupling reaction between 2-pyridylselenyl chloride and Au(I)-bound isonitriles. The reaction involves an initial oxidative addition of the Se-Cl moiety to Au(I), followed by the nucleophilic addition of the pyridine fragment to the isonitrile's C≡N bond, furnishing a metallacycle. Importantly, this is the first example of the pyridine acting as a nucleophile towards metal-bound isonitriles.
View Article and Find Full Text PDFFoods
January 2025
College of Food Science, Southwest University, Chongqing 400715, China.
To investigate the impact of tea polyphenols on the thermodynamic properties, gelatinization properties, rheological properties, and digestion characteristics of starch after ball milling, canna starch and tea polyphenols were mixed at a 10:1 ratio (/) in an experiment and processed with different ball milling times. After ball milling for 3 h, the tea polyphenols and starch fragments formed complexes. Compared with the unmilled mixture, the solubility increased by 199.
View Article and Find Full Text PDFSe Pu
February 2025
CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
Chemical modifications are widely used in research fields such as quantitative proteomics and interaction analyses. Chemical-modification targets can be roughly divided into four categories, including those that integrate isotope labels for quantification purposes, probe the structures of proteins through covalent labeling or cross-linking, incorporate labels to improve the ionization or dissociation of characteristic peptides in complex mixtures, and affinity-enrich various poorly abundant protein translational modifications (PTMs). A chemical modification reaction needs to be simple and efficient for use in proteomics analysis, and should be performed without any complicated process for preparing the labeling reagent.
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