The neuropeptide vasopressin (VP) and its three G protein-coupled receptors (VR, VR and VR) are of high interest in a wide array of drug discovery programs. VR is of particular importance due to its cardiovascular functions and diverse roles in the central nervous system. The structure-activity relationships underpinning ligand-receptor interactions remain however largely unclear, hindering rational drug design. This is not least due to the high structural flexibility of VP in its free as well as receptor-bound states. In this work, we developed a novel approach to reveal features of conformational selectivity upon VP-VR complex formation. We employed virtual screening strategies to probe VP's conformational space for transiently adopted structures that favor binding to VR. To this end, we dissected the VP conformational space into three sub-ensembles, each containing distinct structural sets for VP's three-residue C-terminal tail. We validated the computational results with experimental nuclear magnetic resonance (NMR) data and docked each sub-ensemble to VR. We observed that the conformation of VP's three-residue tail significantly modulated the complex dissociation constants. Solvent-exposed and proline -configured VP tail conformations bound to the receptor with three-fold enhanced affinities compared to compacted or -configured conformations. The solvent-exposed and more flexible structures facilitated unique interaction patterns between VP and VR transmembrane helices 3, 4, and 6 which led to high binding energies. The presented "virtual conformational space screening" approach, integrated with NMR spectroscopy, thus enabled identification and characterization of a conformational selection-type complex formation mechanism that confers novel perspectives on targeting the VP-VR interactions at the level of the encounter complex - an aspect that opens novel research avenues for understanding the functionality of the evolutionary selected conformational properties of VP, as well as guidance for ligand design strategies to provide more potent and selective VP analogues.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8567363 | PMC |
http://dx.doi.org/10.1016/j.csbj.2021.10.024 | DOI Listing |
Acta Crystallogr E Crystallogr Commun
January 2025
A novel coordination compound, [Co()(HO)], was synthesized from aqueous solutions of Co(NO) and the ligand 2-[(5-methyl-1,3,4-thia-diazol-2-yl)sulfan-yl]acetic acid (H, CHNOS). In the monoclinic crystals (space group 2/), the cobalt(II) ion is located about a centre of symmetry and is octa-hedrally coordinated by two anions in a monodentate fashion through carboxyl O atoms and by four water mol-ecules. A relatively strong hydrogen bond between one of the water mol-ecules and the non-coordinating carboxyl-ate O atom consolidates the conformation.
View Article and Find Full Text PDFPLoS One
January 2025
Michael Sayegh Faculty of Pharmacy, Aqaba University of Technology, Aqaba, Jordan.
Breast cancer remains a significant challenge in oncology, highlighting the need for alternative therapeutic strategies that target necroptosis to overcome resistance to conventional therapies. Recent investigations into natural compounds have identified 8,12-dimethoxysanguinarine (SG-A) from Eomecon chionantha as a potential necroptosis inducer. This study presents the first computational exploration of SG-A interactions with key necroptotic proteins-RIPK1, RIPK3, and MLKL-through molecular docking, molecular dynamics (MD), density functional theory (DFT), and molecular electrostatic potential (MEP) analyses.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China.
Accurate protein secondary structure prediction (PSSP) plays a crucial role in biopharmaceutics and disease diagnosis. Current prediction methods are mainly based on multiple sequence alignment (MSA) encoding and collaborative operations of diverse networks. However, existing encoding approaches lead to poor feature space utilization, and encoding quality decreases with fewer homologous proteins.
View Article and Find Full Text PDFBiomolecules
November 2024
Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Rd, Piscataway, NJ 08854, USA.
We demonstrate that a short oligonucleotide complementary to a G-quadruplex domain can invade this iconic, noncanonical DNA secondary structure in ways that profoundly influence the properties and differential occupancies of the resulting DNA polymorphic products. Our spectroscopic mapping of the conformational space of the associated reactants and products, both before and after strand invasion, yield unanticipated outcomes which reveal several overarching features. First, strand invasion induces the disruption of DNA secondary structural elements in both the invading strand (which can assume an iDNA tetrad structure) and the invaded species (a G-quadruplex).
View Article and Find Full Text PDFConnections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!