Role of G protein coupled receptors in acute kidney injury.

Acute kidney injury (AKI) is a clinical condition characterized by a rapid decline in kidney function, which is associated with local inflammation and programmed cell death in the kidney. The G protein-coupled receptors (GPCRs) represent the largest family of signaling transduction proteins in the body, and approximately 40% of drugs on the market target GPCRs. The expressions of various GPCRs, prostaglandin receptors and purinergic receptors, to name a few, are significantly altered in AKI models. And the role of GPCRs in AKI is catching the eyes of researchers due to their distinctive biological functions, such as regulation of hemodynamics, metabolic reprogramming, and inflammation. Therefore, in this review, we aim to discuss the role of GPCRs in the pathogenesis of AKI and summarize the relevant clinical trials involving GPCRs to assess the potential of GPCRs and their ligands as therapeutic targets in AKI and the transition to AKI-CKD.

1,3-Diazepine: A privileged scaffold in medicinal chemistry.

Privileged structures have been widely used as effective templates for drug discovery. While benzo-1,4-diazepine constitutes the first historical example of such a structure, the 1,3 analogue is just as rich in terms of applications in medicinal chemistry. The 1,3-diazepine moiety is present in numerous biological active compounds including natural products, and is used to design compounds displaying a large range of biological activities. It is present in the clinically used anticancer compound pentostatin, in several recent FDA approved ß-lactamase inhibitors (e.g., avibactam) and also in coformycin, a natural product known as a ring-expanded purine analogue displaying antiviral and anticancer activities. Several other 1,3-diazepine containing compounds have entered into clinical trials. This heterocyclic structure has been and is still widely used in medicinal chemistry to design enzyme inhibitors, GPCR ligands, and so forth. This review endeavours to highlight the main use of the 1,3-diazepine scaffold and its derivatives, and their applications in medicinal chemistry, drug design, and therapy. We will focus more particularly on the development of enzyme inhibitors incorporating this scaffold, with a strong emphasis on the molecular interactions involved in the inhibition mechanism.

Self-organization Properties of a GPCR-Binding Peptide with a Fluorinated Tail Studied by Fluorine NMR Spectroscopy.

Conjugation of the bioactive apelin-17 peptide with a fluorocarbon chain results in self-organization of the peptide into micelles. Fluorine NMR spectroscopy studies show that the fluoropeptide's micelles are monodisperse, while proton NMR indicates that the peptide moiety remains largely disordered despite micellization. A very fast exchange rate is measured between the free and micellar states of the peptide which enables the number of molecules present in the micelle to be estimated as 200, in agreement with values found by dynamic light scattering measurements.

Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition.

In the last decade, machine learning and artificial intelligence applications have received a significant boost in performance and attention in both academic research and industry. The success behind most of the recent state-of-the-art methods can be attributed to the latest developments in deep learning. When applied to various scientific domains that are concerned with the processing of non-tabular data, for example, image or text, deep learning has been shown to outperform not only conventional machine learning but also highly specialized tools developed by domain experts. This review aims to summarize AI-based research for GPCR bioactive ligand discovery with a particular focus on the most recent achievements and research trends. To make this article accessible to a broad audience of computational scientists, we provide instructive explanations of the underlying methodology, including overviews of the most commonly used deep learning architectures and feature representations of molecular data. We highlight the latest AI-based research that has led to the successful discovery of GPCR bioactive ligands. However, an equal focus of this review is on the discussion of machine learning-based technology that has been applied to ligand discovery in general and has the potential to pave the way for successful GPCR bioactive ligand discovery in the future. This review concludes with a brief outlook highlighting the recent research trends in deep learning, such as active learning and semi-supervised learning, which have great potential for advancing bioactive ligand discovery.

Neurotensin Analogues Containing Cyclic Surrogates of Tyrosine at Position 11 Improve NTS2 Selectivity Leading to Analgesia without Hypotension and Hypothermia.

Neurotensin (NT) exerts its analgesic effects through activation of the G protein-coupled receptors NTS1 and NTS2. This opioid-independent antinociception represents a potential alternative for pain management. While activation of NTS1 also induces a drop in blood pressure and body temperature, NTS2 appears to be an analgesic target free of these adverse effects. Here, we report modifications of NT at Tyr11 to increase selectivity toward NTS2, complemented by modifications at the N-terminus to impair proteolytic degradation of the biologically active NT(8-13) sequence. Replacement of Tyr11 by either 6-OH-Tic or 7-OH-Tic resulted in a significant loss of binding affinity to NTS1 and subsequent NTS2 selectivity. Incorporation of the unnatural amino acid ß3hLys at position 8 increased the half-life to over 24 h in plasma. Simultaneous integration of both ß3hLys8 and 6-OH-Tic11 into NT(8-13) produced a potent and NTS2-selective analogue with strong analgesic action after intrathecal delivery in the rat formalin-induced pain model with an ED50 of 1.4 nmol. Additionally, intravenous administration of this NT analogue did not produce persistent hypotension or hypothermia. These results demonstrate that NT analogues harboring unnatural amino acids at positions 8 and 11 can enhance crucial pharmacokinetic and pharmacodynamic features for NT(8-13) analogues, i.e., proteolytic stability, NTS2 selectivity, and improved analgesic/adverse effect ratio.

Structure-based exploration of an allosteric binding pocket in the NTS1 receptor using bitopic NT(8-13) derivatives and molecular dynamics simulations.

Crystal structures of neurotensin receptor subtype 1 (NTS1) allowed us to visualize the binding mode of the endogenous peptide hormone neurotensin and its pharmacologically active C-terminal fragment NT(8-13) within the orthosteric binding pocket of NTS1. Beneath the orthosteric binding pocket, we detected a cavity that exhibits different sequences in the neurotensin receptor subtypes NTS1 and NTS2. In this study, we explored this allosteric binding pocket using bitopic test peptides of type NT(8-13)-Xaa, in which the C-terminal part of NT(8-13) is connected to different amino acids that extend into the newly discovered pocket. Our test compounds showed nanomolar affinities for NTS1, a measurable increase in subtype selectivity compared to the parent peptide NT(8-13), and the capacity to activate the receptor in an IP accumulation assay. Computational investigation of the selected test compounds at NTS1 showed a conserved binding mode within the orthosteric binding pocket, whereas the allosteric cavity was able to adapt to different residues, which suggests a high degree of structural plasticity within that cavity of NTS1.

Unveiling novel 2-cyclopropyl-3-ethynyl-4-(4-fluorophenyl)quinolines as GPCR ligands via PI3-kinase/PAR-1 antagonism and platelet aggregation valuations; development of a new class of anticancer drugs with thrombolytic effects.

In the present study, novel 2-cyclopropyl-3-ethynyl-4-(4-fluorophenyl) quinolines (4a-l) were recognized and evaluated as G-Protein Coupled Receptor (GPCR) ligands through molecular evaluations. Thrombin mediates adhesion of mast cell, a type of cell abundantly found in connective tissue and releasing histamine and other substances during inflammatory and allergic reactions, through phosphoinositol 3-kinase pathway. With this background, as preliminary, 4a-l are resolute to be potential leads, designated from their effective phosphoinositol 3-kinase (PI3-Kinase) inhibition potentials, best-docked scores, comparative ligand efficiency, and significant structural attributes evaluated by ab initio simulations. Since thrombin is one of the main reason for various cancer invasion in association with PI3Kinase, a thrombolytic potential of the compounds also analyzed. The experimental in vitro studies confirmed the significant enhancement as PI3Kinase inhibitors and appreciable enhancement in MTT assay of breast and skin cancer cell lines. Significantly, acetophenone substituent in the quinoline scaffold could be coherent to note the significant binding affinity to all the evaluated drug targets.

Chemical space screening around Phe3 in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings.

In this study, affinities and activities of derivatized analogues of Dmt-dermorphin[1-4] (i.e. Dmt-d-Ala-Phe-GlyNH2, Dmt = 2',6'-dimethyl-(S)-tyrosine) for the µ opioid receptor (MOP) and δ opioid receptor (DOP) were evaluated using radioligand binding studies, functional cell-based assays and isolated organ bath experiments. By means of solid-phase or solution-phase Suzuki-Miyaura cross-couplings, various substituted regioisomers of the phenylalanine moiety in position 3 of the sequence were prepared. An 18-membered library of opioid tetrapeptides was generated via screening of the chemical space around the Phe3 side chain. These substitutions modulated bioactivity, receptor subtype selectivity and highly effective ligands with subnanomolar binding affinities, contributed to higher functional activities and potent analgesic actions. In search of selective peptidic ligands, we show here that the Suzuki-Miyaura reaction is a versatile and robust tool which could also be deployed elsewhere.

Quo vadis G protein-coupled receptor ligands? A tool for analysis of the emergence of new groups of compounds over time.

Exponential growth in the number of compounds with experimentally verified activity towards particular target has led to the emergence of various databases gathering data on biological activity. In this study, the ligands of family A of the G Protein-Coupled Receptors that are collected in the ChEMBL database were examined, and special attention was given to serotonin receptors. Sets of compounds were examined in terms of their appearance over time, they were mapped to the chemical space of drugs deposited in DrugBank, and the emergence of structurally new clusters of compounds was indicated. In addition, a tool for detailed analysis of the obtained visualizations was prepared and made available online at http://chem.gmum.net/vischem, which enables the investigation of chemical structures while referring to particular data points depicted in the figures and changes in compounds datasets over time.

Optimization of on-resin palladium-catalyzed Sonogashira cross-coupling reaction for peptides and its use in a structure-activity relationship study of a class B GPCR ligand.

Class B G protein-coupled receptors are activated by their cognate ligands following a two-step binding model involving a specific network of ligand-receptor intermolecular interactions. In particular, a N-capping structure present in the ligand would contribute significantly to position the N-terminal segment of the ligand once bound to its receptor. The aim of the current study was to implement the use of Pd-catalyzed Sonogashira coupling for the investigation of this structural motif. First, we have developed and evaluated various Sonogashira-based procedures for on-resin post-synthesis modification using a Leu-enkephalin derivative as a model peptide. Next, we have prepared a small library of PACAP-based analogs and evaluated the pharmacological profile of a few of them using a competitive binding assay, as well as functional and survival assays. Notably, our results suggest that the modification of the N-capping region could alter the binding specificity of PACAP without altering its biological activity, thereby opening the way for the design of more selective compounds. Finally, the possibility to achieve sequential multiple point substitutions via the Sonogashira cross-coupling method, during solid phase peptide synthesis, was also evaluated. Altogether, we demonstrated the versatility of such a procedure for the incorporation of various mono- and multiple alkyne-derived modifications during solid phase peptide synthesis and confirmed its usefulness for the structure-activity study of a class B GPCR ligand.

Multitarget-directed tricyclic pyridazinones as G protein-coupled receptor ligands and cholinesterase inhibitors.

By following a multitarget ligand design approach, a library of 47 compounds was prepared, and they were tested as binders of selected G protein-coupled receptors (GPCRs) and inhibitors of acetyl and/or butyryl cholinesterase. The newly designed ligands feature pyridazinone-based tricyclic scaffolds connected through alkyl chains of variable length to proper amine moieties (e.g., substituted piperazines or piperidines) for GPCR and cholinesterase (ChE) molecular recognition. The compounds were tested at three different GPCRs, namely serotoninergic 5-HT1A, adrenergic α1A, and dopaminergic D2 receptors. Our main goal was the discovery of compounds that exhibit, in addition to ChE inhibition, antagonist activity at 5-HT1A because of its involvement in neuronal deficits typical of Alzheimer's and other neurodegenerative diseases. Ligands with nanomolar affinity for the tested GPCRs were discovered, but most of them behaved as dual antagonists of α1A and 5-HT1A receptors. Nevertheless, several compounds displaying this GPCR affinity profile also showed moderate to good inhibition of AChE and BChE, thus deserving further investigations to exploit the therapeutic potential of such unusual biological profiles.