Native mass spectrometry (MS) is a powerful analytical technique to directly probe noncovalent protein-protein and protein-ligand interactions. However, not every MS platform can preserve proteins in their native conformation due to high energy deposition from the utilized ionization source. Most small molecules approved as drugs and in development interact with their targets through noncovalent interactions. Therefore, rapid methods to analyze noncovalent protein-ligand interactions are necessary for the early stages of the drug discovery pipeline. Herein, we describe a method for analyzing noncovalent protein-ligand complexes by IR-MALDESI-MS with analysis times of ∼13 s per sample. Carbonic anhydrase and the kinase domain of Bruton's tyrosine kinase are paired with known noncovalent binders to evaluate the effectiveness of native MS by IR-MALDESI.
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http://dx.doi.org/10.1021/jasms.4c00199 | 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 PDFBiophys Chem
December 2024
Department of Chemistry and Center for Atomic, Molecular, Optical Sciences and Technologies (CAMOST), Indian Institute of Science, Education and Research (IISER) Tirupati, Yerpedu Mandal, Tirupati 517619, India. Electronic address:
Serotonin-receptor binding plays a key role in several neurological and biological processes, including mood, sleep, hunger, cognition, learning, and memory. In this article, we performed molecular dynamics simulation to examine the key residues that play an essential role in the binding of serotonin to the G-protein-coupled 5-HT receptor (5HTR) via electrostatic interactions. Key residues for electrostatic interactions were identified via bond distance analysis and frustration analysis methods.
View Article and Find Full Text PDFJ Biomol Struct Dyn
December 2024
Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamilnadu, India.
Angew Chem Int Ed Engl
December 2024
Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy.
We introduce the fragment-pairwise Local Energy Decomposition (fp-LED) scheme for precise quantification of individual interactions contributing to the binding energy of arbitrary chemical entities, such as protein-ligand binding energies, lattice energies of molecular crystals, or association energies of large biomolecular assemblies. Using fp-LED, we can assess whether the contribution to the binding energy arising from noncovalent interactions between pairs of molecular fragments in any chemical system is attractive or repulsive, and accurately quantify its magnitude at the coupled cluster level - commonly considered as the "gold standard" of computational chemistry. Such insights are crucial for advancing molecular and material design strategies in fields like catalysis and therapeutic development.
View Article and Find Full Text PDFbioRxiv
November 2024
Department of Chemistry, Dartmouth College, Hanover, NH, USA.
Intrinsically disordered proteins are implicated in many human diseases. Small molecules that target the disordered androgen receptor transactivation domain have entered human trials for the treatment of castration-resistant prostate cancer. These molecules have been shown to react with cysteine residues of the androgen receptor transactivation domain and form covalent adducts under physiological conditions.
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