Allosteric coupling and biased agonism in G protein‐coupled receptors

G protein-coupled receptors (GPCRs) are essential cell membrane signaling molecules and represent the most important class of drug targets. Some signaling pathways downstream of a GPCR may be responsible for drug adverse effects, while others mediate therapeutic efficacy. Biased ligands preferentially activate only a subset of all GPCR signaling pathways. They hold great potential to become next-generation GPCR drugs with less side effects due to their potential to exclusively activate desired signaling pathways. However, the molecular basis of biased agonism is poorly understood. GPCR activation occurs through allosteric coupling, the propagation of conformational changes from the extracellular ligand-binding pocket to the intracellular G protein-binding interface. Comparison of GPCR structures in complex with G proteins or beta-arrestin reveals that intracellular transducer coupling results in closure of the ligand-binding pocket trapping the agonist inside its binding site. Allosteric coupling appears to be transducer-specific offering the possibility of harnessing this mechanism for the design of biased ligands. Here, we review the biochemical, pharmacological, structural, and biophysical evidence for allosteric coupling and delineate that biased agonism should be a consequence of preferential allosteric coupling from the ligand-binding pocket to one transducer-binding site. As transducer binding leads to large structural rearrangements in the extracellular ligand-binding pocket, we survey biased ligands with an extended binding mode that interact with extracellular receptor domains. We propose that biased ligands use ligand-specific triggers inside the binding pocket that are relayed through preferential allosteric coupling to a specific transducer, eventually leading to biased signaling

Structural determinants of sphingosine-1-phosphate receptor selectivity

Fingolimod, the prodrug of fingolimod-1-phosphate (F1P), was the first sphingosine-1-phosphate receptor (S1PR) modulator approved for multiple sclerosis. F1P unselectively targets all five S1PR subtypes. While agonism (functional antagonism via receptor internalization) at S1PR1 leads to the desired immune modulatory effects, agonism at S1PR3 is associated with cardiac adverse effects. This motivated the development of S1PR3-sparing compounds and led to a second generation of S1PR1,5-selective ligands like siponimod and ozanimod. Our method combines molecular dynamics simulations and three-dimensional pharmacophores (dynophores) and enables the elucidation of S1PR subtype-specific binding site characteristics, visualizing also subtle differences in receptor–ligand interactions. F1P and the endogenous ligand sphingosine-1-phosphate bind to the orthosteric pocket of all S1PRs, but show different binding mode dynamics, uncovering potential starting points for the development of subtype-specific ligands. Our study contributes to the mechanistic understanding of the selectivity profile of approved drugs like ozanimod and siponimod and pharmaceutical tool compounds like CYM5541

Mechanistic Understanding of Peptide Analogues, DALDA, [Dmt1]DALDA, and KGOP01, Binding to the Mu Opioid Receptor

The mu opioid receptor (MOR) is the primary target for analgesia of endogenous opioid peptides, alkaloids, synthetic small molecules with diverse scaffolds, and peptidomimetics. Peptide-based opioids are viewed as potential analgesics with reduced side effects and have received constant scientific interest over the years. This study focuses on three potent peptide and peptidomimetic MOR agonists, DALDA, [Dmt1]DALDA, and KGOP01, and the prototypical peptide MOR agonist DAMGO. We present the first molecular modeling study and structure–activity relationships aided by in vitro assays and molecular docking of the opioid peptide analogues, in order to gain insight into their mode of binding to the MOR. In vitro binding and functional assays revealed the same rank order with KGOP01 > [Dmt1]DALDA > DAMGO > DALDA for both binding and MOR activation. Using molecular docking at the MOR and three-dimensional interaction pattern analysis, we have rationalized the experimental outcomes and highlighted key amino acid residues responsible for agonist binding to the MOR. The Dmt (2′,6′-dimethyl-L-Tyr) moiety of [Dmt1]DALDA and KGOP01 was found to represent the driving force for their high potency and agonist activity at the MOR. These findings contribute to a deeper understanding of MOR function and flexible peptide ligand–MOR interactions, that are of significant relevance for the future design of opioid peptide-based analgesics

Biased Ligands Differentially Shape the Conformation of the Extracellular Loop Region in 5-HT2B Receptors

G protein-coupled receptors are linked to various intracellular transducers, each pathway associated with different physiological effects. Biased ligands, capable of activating one pathway over another, are gaining attention for their therapeutic potential, as they could selectively activate beneficial pathways whilst avoiding those responsible for adverse effects. We performed molecular dynamics simulations with known β-arrestin-biased ligands like lysergic acid diethylamide and ergotamine in complex with the 5-HT2B receptor and discovered that the extent of ligand bias is directly connected with the degree of closure of the extracellular loop region. Given a loose allosteric coupling of extracellular and intracellular receptor regions, we delineate a concept for biased signaling at serotonin receptors, by which conformational interference with binding pocket closure restricts the signaling repertoire of the receptor. Molecular docking studies of biased ligands gathered from the BiasDB demonstrate that larger ligands only show plausible docking poses in the ergotamine-bound structure, highlighting the conformational constraints associated with bias. This emphasizes the importance of selecting the appropriate receptor conformation on which to base virtual screening workflows in structure-based drug design of biased ligands. As this mechanism of ligand bias has also been observed for muscarinic receptors, our studies provide a general mechanism of signaling bias transferable between aminergic receptors

Biological characterization, mechanistic investigation and structure‐activity relationships of chemically stable TLR2 antagonists

Toll‐like receptors (TLRs) build the first barrier in the innate immune response and therefore represent promising targets for the modulation of inflammatory processes. Recently, the pyrogallol‐containing TLR2 antagonists CU‐CPT22 and MMG‐11 were reported; however, their 1,2,3‐triphenol motif renders them highly susceptible to oxidation and excludes them from use in extended experiments under aerobic conditions. Therefore, we have developed a set of novel TLR2 antagonists (1 –9 ) based on the systematic variation of substructures, linker elements, and the hydrogen‐bonding pattern of the pyrogallol precursors by using chemically robust building blocks. The novel series of chemically stable and synthetically accessible TLR2 antagonists (1 –9 ) was pharmacologically characterized, and the potential binding modes of the active compounds were evaluated structurally. Our results provide new insights into structure‐activity relationships and allow rationalization of structural binding characteristics. Moreover, they support the hypothesis that this class of TLR ligands bind solely to TLR2 and do not directly interact with TLR1 or TLR6 of the functional heterodimer. The most active compound from this series (6 ), is chemically stable, nontoxic, TLR2‐selective, and shows a similar activity with regard to the pyrogallol starting points, thus indicating the variability of the hydrogen bonding pattern

Next generation 3D pharmacophore modeling

3D pharmacophore models are three‐dimensional ensembles of chemically defined interactions of a ligand in its bioactive conformation. They represent an elegant way to decipher chemically encoded ligand information and have therefore become a valuable tool in drug design. In this review, we provide an overview on the basic concept of this method and summarize key studies for applying 3D pharmacophore models in virtual screening and mechanistic studies for protein functionality. Moreover, we discuss recent developments in the field. The combination of 3D pharmacophore models with molecular dynamics simulations could be a quantum leap forward since these approaches consider macromolecule–ligand interactions as dynamic and therefore show a physiologically relevant interaction pattern. Other trends include the efficient usage of 3D pharmacophore information in machine learning and artificial intelligence applications or freely accessible web servers for 3D pharmacophore modeling. The recent developments show that 3D pharmacophore modeling is a vibrant field with various applications in drug discovery and beyond

Simulación de la cámara de combustión de una caldera pitotubular utilizando la herramienta computacional ansys

This article analyzes the combustion reaction between the fuel (ACPM) and combustion (AIR) that occurs inside the combustion chamber of a pyrotubular boiler using Ansys® software and selecting the fluent method (CFD), being the indicated one To simulate fluids. A study of the behavior of the temperature and pressure through the total length of the combustion chamber and in turn the molar and mass fractions of the products resulting from the combustion. The results of the variables were compared with the approach of a mathematical model implemented in the simulink tool, taking into account the same conditions and the ACPM fuel.En este artículo se analiza la reacción de combustión entre el combustible (ACPM) y comburente (AIRE) que ocurre al interior de la cámara de combustión de una caldera piro tubular empleando el software Ansys® y seleccionando el método fluent (CFD) [2], siendo el indicado para simular fluidos en procesos de combustión. Se realizó un estudio del comportamiento de la temperatura y presión a través de la longitud total de la cámara de combustión y a su vez las fracciones molares y másicas de los productos resultantes de la combustión ,,  Y . Los resultados de las variables fueron comparados con el desarrollo de un modelo matemático implementado en la herramienta Simulink®, teniendo en cuenta las mismas condiciones y el combustible ACPM.

Multiwavelength excitation Raman scattering analysis of bulk and 2 dimensional MoS2: vibrational properties of atomically thin MoS2 layers

In order to deepen the knowledge of the vibrational properties of two-dimensional (2D) MoS2 atomic layers, a complete and systematic Raman scattering analysis has been performed using both bulk single-crystal MoS2 samples and atomically thin MoS2 layers. Raman spectra have been measured under non-resonant and resonant conditions using seven different excitation wavelengths from near-infrared (NIR) to ultraviolet (UV). These measurements have allowed us to observe and identify 41 peaks, among which 22 have not been previously experimentally observed for this compound, and characterize the existence of different resonant excitation conditions for the different excitation wavelengths. This has also included the first analysis of resonant Raman spectra that are achieved using UV excitation conditions. In addition, the analysis of atomically thin MoS2 layers has corroborated the higher potential of UV resonant Raman scattering measurements for the non-destructive assessment of 2D MoS2 samples. Analysis of the relative integral intensity of the additional first- and second-order peaks measured under UV resonant excitation conditions is proposed for the non-destructive characterization of the thickness of the layers, complementing previous studies based on the changes of the peak frequencies