Study Of Receptor-ligand Interactions Research Articles

Molecular designing and in silico evaluation of darunavir derivatives as anticancer agents.

Darunavir is a synthetic nonpeptidic protease inhibitor which has been tested for anticancer properties. To deduce and enhance the anticancer activity of the Darunavir, we have modified its reactive moiety in an effective way. We designed 9 analogues in ChemBioOffice 2010 and minimized using the LigPrep tool of Schrödinger 2011. These analogues can obstruct the activity of other signalling pathways which are implicated in many tumors. Results of the QikProp showed that all the analogues lied in the specified range of all the pharmacokinetic (ADMET) properties required to become the successful drug. Docking study was performed to test its anticancer activity against the biomarkers of the five main types of cancers i.e. bone, brain, breast, colon and skin cancer. Grid was generated for each oncoproteins by specifying the active site amino acids. The binding model of best scoring analogue with each protein was assessed from their G-scores and disclosed by docking analysis using the XP visualizer tool. An analysis of the receptor-ligand interaction studies revealed that these nine Darunavir analogues are active against all cancer biomarkers and have the features to prove themselves as anticancer drugs, further to be synthesized and tested against the cell lines.

Using the newly developed nanoluciferase as an ultrasensitive bioluminescent probe for ligand-receptor interaction studies

Nanoluciferase (NanoLuc) is a newly developed small monomeric luciferase reporter with the brightest bioluminescence reported to date. Recently, we have used NanoLuc as a novel ultrasensitive bioluminescent probe for ligand-receptor interaction studies. In the present highlight, I discuss its general application in ligand-receptor interactions and other binding studies. This novel ultrasensitive bioluminescent probe will facilitate a wide range of biological studies as its new applications are continuously developed.

A Microfluidic Platform for Controlled Ligand Exposure and Visualization of Cellular Response

We report here a microfluidic device with a unique architecture for capturing and isolating single cells, as well as providing strict control of reagent delivery to the cells. The device contains individualized cell traps with multiple inlet channels to allow flow-focusing of reagents for controlled ligand-receptor interaction studies. In this configuration, a change in relative inlet pressures causes immediate change in the relative widths of the reagent streams which allows timed exposure of cells to ligands of interest. We demonstrate the capabilities of this device by imaging cellular calcium response as a function of ligand pulse width, inter-pulse interval, and frequency. Rat basophilic leukemia (RBL) cells that endogenously express the IgE receptor are loaded with Fluo-4, a calcium indicator dye, and then captured in the device traps. Cells were systematically exposed to various ligand (multivalent crosslinker DNP-BSA) pulse widths (5 seconds to 2 minutes) and calcium response monitored with high-resolution fluorescence imaging. A significant delay between initial ligand exposure and calcium mobilization was observed. The relationship between pulse width, inter-pulse interval, and frequency and the temporal profile of the calcium response is currently under investigation.

β-Barrel scaffolds for the grafting of extracellular loops from G-protein-coupled receptors

Owing to the difficulties in production and purification of G-protein-coupled receptors (GPCRs), relatively little structural information is available about this class of receptors. Here we aim at developing small chimeric proteins, displaying the extracellular ligand-binding motifs of a human GPCR, the Y receptor. This allows the study of ligand-receptor interactions in simplified systems. We present comprehensive information on the use of transmembrane (OmpA) and soluble (Blc) β-barrel scaffolds. Whereas Blc appeared to be not fully compatible with our approach, owing to problems with refolding of the hybrid constructs, loop-grafted versions of OmpA delivered encouraging results. Previously, we described a chimeric construct based on OmpA displaying all three extracellular Y1 receptor loops in different topologies and showing moderate affinity to one of the natural ligands. Now, we present detailed data on the interaction of these constructs with several Y receptor ligands along with data on new constructs. Our findings suggest a common binding mode for all ligands, which is mediated through the C-terminal residues of the peptide ligand, supporting the functional validity of these hybrid receptors. The observed binding affinities, however, are well below those observed for the natural receptors, clearly indicating limitations in mimicking the natural systems.

Modeling and Simulation Studies of Human β3 Adrenergic Receptor and its Interactions with Agonists

β3 adrenergic receptor (β3AR) is known to mediate various pharmacological and physiological effects such as thermogenesis in brown adipocytes, lipolysis in white adipocytes, glucose homeostasis and intestinal smooth muscle relaxation. Several efforts have been made in this field to understand their function and regulation in different human tissues and they have emerged as potential attractive targets in drug discovery for the treatment of diabetes, depression, obesity etc. Although the crystal structures of Bovine Rhodopsin and β2 adrenergic receptor have been resolved, to date there is no three dimensional structural information on β3AR. Our aim in this study was to model 3D structure of β3AR by various molecular modeling and simulation techniques. In this paper, we describe a refined predicted model of β3AR using different algorithms for structure prediction. The structural refinement and minimization of the generated 3D model of β3AR were done by Schrodinger suite 9.1. Docking studies of β3AR model with the known agonists enabled us to identify specific residues, viz, Asp 117, Ser 208, Ser 209, Ser 212, Arg 315, Asn 332, within the β3AR binding pocket, which might play an important role in ligand binding. Receptor ligand interaction studies clearly indicated that these five residues showed strong hydrogen bonding interactions with the ligands. The results have been correlated with the experimental data available. The predicted ligand binding interactions and the simulation studies validate the methods used to predict the 3D-structure.

TATA Binding Proteins Can Recognize Nontraditional DNA Sequences

We demonstrate an accurate, quantitative, and label-free optical technology for high-throughput studies of receptor-ligand interactions, and apply it to TATA binding protein (TBP) interactions with oligonucleotides. We present a simple method to prepare single-stranded and double-stranded DNA microarrays with comparable surface density, ensuring an accurate comparison of TBP activity with both types of DNA. In particular, we find that TBP binds tightly to single-stranded DNA, especially to stretches of polythymine (poly-T), as well as to the traditional TATA box. We further investigate the correlation of TBP activity with various lengths of DNA and find that the number of TBPs bound to DNA increases >7-fold as the oligomer length increases from 9 to 40. Finally, we perform a full human genome analysis and discover that 35.5% of human promoters have poly-T stretches. In summary, we report, for the first time to our knowledge, the activity of TBP with poly-T stretches by presenting an elegant stepwise analysis of multiple techniques: discovery by a novel quantitative detection of microarrays, confirmation by a traditional gel electrophoresis, and a full genome prediction with computational analyses.

Design, recombinant expression and convenient A‐chain N‐terminal europium‐labelling of a fully active human relaxin‐3 analogue

Relaxin-3 (also known as INSL7) is a recently identified neuropeptide belonging to the insulin/relaxin superfamily. It plays a putative role in the regulation of food intake, in the stress response and in reproduction by activating the G-protein-coupled receptor, RXFP3. In a previous study, we prepared 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)/Eu(3+)-labelled human relaxin-3 as a tracer for the study of ligand-receptor interactions, which necessitated a complicated site-specific labelling strategy because human relaxin-3 contains four primary amine moieties, all of which react with the primary amine-specific modification reagent. To simplify the labelling procedure, in the present study we created an easily labelled, recombinant analogue of human relaxin-3 with only one primary amine moiety at the A-chain N-terminus. The analogue retained full activity and could be easily labelled by various functional probes at the A-chain N-terminus. The DOTA/Eu(3+)-labelled analogue retained high binding affinity for its cognate receptor, RXFP3, and thus represents a useful, nonradioactive and stable tracer for studying the interaction of RXFP3 with various natural or synthetic ligands. This new analogue is also a suitable template for the design of other relaxin-3 analogues that can be easily labelled with the DOTA/Eu(3+) moiety and used to study binding activity and interactions with various RXFP3 analogues in the future.

A novel fluorescent histamine H1 receptor antagonist demonstrates the advantage of using fluorescence correlation spectroscopy to study the binding of lipophilic ligands

Fluorescent ligands facilitate the study of ligand-receptor interactions at the level of single cells and individual receptors. Here, we describe a novel fluorescent histamine H(1) receptor antagonist (mepyramine-BODIPY630-650) and use it to monitor the membrane diffusion of the histamine H(1) receptor. The human histamine H(1) receptor fused to yellow fluorescent protein (YFP) was transiently expressed in CHO-K1 cells. The time course of binding of mepyramine-BODIPY630-650 to the H(1) receptor was determined by confocal microscopy. Additionally, fluorescence correlation spectroscopy (FCS) was used to characterize the diffusion coefficient of the H(1) receptor in cell membranes both directly (YFP fluorescence) and in its antagonist-bound state (with mepyramine-BODIPY630-650). Mepyramine-BODIPY630-650 was a high-affinity antagonist at the histamine H(1) receptor. Specific membrane binding, in addition to significant intracellular uptake of the fluorescent ligand, was detected by confocal microscopy. However, FCS was able to quantify the receptor-specific binding in the membrane, as well as the diffusion coefficient of the antagonist-H(1) receptor-YFP complexes, which was significantly slower than when determined directly using YFP. FCS also detected specific binding of mepyramine-BODIPY630-650 to the endogenous H(1) receptor in HeLa cells. Mepyramine-BODIPY630-650 is a useful tool for localizing the H(1) receptor using confocal microscopy. However, its use in conjunction with FCS allows quantification of ligand binding at the membrane, as well as determining receptor diffusion in the absence of significant bleaching effects. Finally, these methods can be successfully extended to endogenously expressed untagged receptors in HeLa cells.

Revealing a steroid receptor ligand as a unique PPARγ agonist

Peroxisome proliferator-activated receptor gamma (PPARγ) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPARγ agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPARγ target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPARγ ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPARγ ligands in the treatment of insulin resistance.

Structural Basis for Iloprost as a Dual Peroxisome Proliferator-activated Receptor α/δ Agonist

Iloprost is a prostacyclin analog that has been used to treat many vascular conditions. Peroxisome proliferator-activated receptors (PPARs) are ligand-regulated transcription factors with various important biological effects such as metabolic and cardiovascular physiology. Here, we report the crystal structures of the PPARα ligand-binding domain and PPARδ ligand-binding domain bound to iloprost, thus providing unambiguous evidence for the direct interaction between iloprost and PPARs and a structural basis for the recognition of PPARα/δ by this prostacyclin analog. In addition to conserved contacts for all PPARα ligands, iloprost also initiates several specific interactions with PPARs using its unique structural groups. Structural and functional studies of receptor-ligand interactions reveal strong functional correlations of the iloprost-PPARα/δ interactions as well as the molecular basis of PPAR subtype selectivity toward iloprost ligand. As such, the structural mechanism may provide a more rational template for designing novel compounds targeting PPARs with more favorable pharmacologic impact based on existing iloprost drugs.

New NMR tools for the study of receptor-ligand interactions in non-homogenous media

New NMR tools for the study of receptor-ligand interactions in non-homogenous media

Computational analysis of the binding ability of heterocyclic and conformationally constrained epibatidine analogs in the neuronal nicotinic acetylcholine receptor

One of the most critical issues on the study of ligand-receptor interactions in drug design is the knowledge of the bioactive conformation of the ligand. In this study, we describe a computational approach aimed at estimating the binding ability of epibatidine analogs to interact with the neuronal nicotinic acetylcholine receptor (nAChR) and get insights into the bioactive conformation. The protocol followed consists of a docking analysis and evaluation of pharmacophore parameters of the docked structures. On the basis of the biological data, the results have revealed that the docking analysis is able to predict active ligands, whereas further efforts are needed to develop a suitable and solid pharmacophore model.

Molecular recognition of nitrated fatty acids by PPARγ

Peroxisome proliferator activated receptor-γ (PPARγ) regulates metabolic homeostasis and adipocyte differentiation, and it is activated by oxidized and nitrated fatty acids. Here we report the crystal structure of the PPARγ ligand binding domain bound to nitrated linoleic acid, a potent endogenous ligand of PPARγ. Structural and functional studies of receptor-ligand interactions reveal the molecular basis of PPARγ discrimination of various naturally occurring fatty acid derivatives.

Molecular recognition in the sphingosine 1-phosphate receptor family

Computational modeling and its application in ligand screening and ligand receptor interaction studies play important roles in structure-based drug design. A series of sphingosine 1-phosphate (S1P) receptor ligands with varying potencies and receptor selectivities were docked into homology models of the S1P 1–5 receptors. These studies provided molecular insights into pharmacological trends both across the receptor family as well as at single receptors. This study identifies ligand recognition features that generalize across the S1P receptor family, features unique to the S1P 4 and S1P 5 receptors, and suggests significant structural differences of the S1P 2 receptor. Docking results reveal a previously unknown sulfur–aromatic interaction between the S1P 4 C5.44 sulfur atom and the phenyl ring of benzimidazole as well as π–π interaction between F3.33 of S1P 1,4,5 and aromatic ligands. The findings not only confirm the importance of a cation–π interaction between W4.64 and the ammonium of S1P at S1P 4 but also predict the same interaction at S1P 5. S1P receptor models are validated for pharmacophore development including database mining and new ligand discovery and serve as tools for ligand optimization to improve potency and selectivity.

A Two-Photon Excitation Fluorescence Cross-Correlation Assay for a Model Ligand-Receptor Binding System Using Quantum Dots

Two-photon excitation fluorescence cross-correlation spectroscopy (TPE-XCS) is a very suitable method for studying interactions of two distinctly labeled fluorescent molecules. As such, it lends itself nicely to the study of ligand-receptor interactions. By labeling the ligand with one color of fluorescent dye and the receptor with another, it is possible to directly monitor ligand binding rather than inferring binding by monitoring downstream effects. One challenge of the TPE-XCS approach is that of separating the signal due to the receptor from that of the ligand. Using standard organic fluorescent labels there is almost inevitably spectral cross talk between the detection channels, which must be accounted for in TPE-XCS data analysis. However, using quantum dots as labels for both ligand and receptor this limitation can be alleviated, because of the dot's narrower emission spectra. Using solely quantum dots as fluorescent labels is a novel approach to TPE-XCS, which may be generalizable to many pairs of interacting biomolecules after the proof of principle and the assessment of limitations presented here. Moreover, it is essential that relevant pharmacological parameters such as the equilibrium dissociation constant, K d, can be easily extracted from the XCS data with minimal processing. Herein, we present a modified expression for fractional occupancy based on the auto- and cross-correlation decays obtained from a well-defined ligand-receptor system. Nanocrystalline semiconductor quantum dots functionalized with biotin ( λ em = 605 nm) and streptavidin ( λ em = 525 nm) were used for which an average K d value of 0.30 ± 0.04 × 10 −9 M was obtained (cf. native system ∼10 −15). Additionally, the off-rate coefficient ( k off) for dissociation of the two quantum dots was determined as 5 × 10 −5 s −1. This off-rate is slightly larger than for native biotin-streptavidin (5 × 10 −6 s −1); the bulky nature of the quantum dots and restricted motion/orientation of functionalized dots in solution can account for differences in the streptavidin-biotin mediated dot-dot binding compared with those for native streptavidin-biotin.

Microplate gel-filtration method for radioligand-binding assays

A thin-layer gel-filtration chromatographic method has been developed in a 96-well format to separate free and protein-bound ligand in radioligand-binding assays. The mobile phase in the gel-filtration plate is removed via quick centrifugation before samples are applied. Protein-bound ligand is recovered via centrifugation into another 96-well plate for radioactivity measurements. The method exhibits excellent recovery of protein-ligand complexes and less opportunity for dissociation of the complexes since it eliminates major dilution effects from the mobile phase of a column and from elution steps in conventional gel-filtration chromatography. It offers other advantages: simple, rapid, inexpensive, quantitative, and able to handle a large number of samples as required in drug discovery and clinical settings. This microplate gel-filtration method was optimized in studies of receptor-ligand interactions using estrogen receptors as examples and can be used in other radioligand-binding assays.

Molecular dynamics simulation for ligand-receptor studies. Carbohydrates interactions in aqueous solutions.

The review deals with the problem of the study of ligand-receptor interactions and the use of Molecular Dynamics (MD) simulation to approach such a problem. After a short review of the fundamentals of MD we describe the medium in which all biology takes place, water. Emphasis is put on the water models appropriate for simulation of macromolecular systems explicitly including the water molecules. We consider the quality of the water model both in terms of simplicity and performance to describe the liquid water properties. Heavy water, although not a biologically viable medium, is considered since many experiments make use of it as a solvent. Sweetness of carbohydrates is considered as an example of the procedure suitable to characterize active sites on the ligands. Consideration is given to the computation of the binding constants through molecular dynamics. The computation of the Free Energy is described and illustrated. The potentiality of MD for studies of ligand-receptor interactions is limited by the computer resources, for even with large computing facilities the need of relatively long simulation times severely restricts the study of large systems. A method is described in which several shells are treated at different levels of approximation, form mechanical response and mean electrical field to quantum mechanics, through stochastic dynamics and atomic classical MD. The review closes with a brief account of the perspectives of the method.

Direct studies of ligand-receptor interactions and ion channel blocking (Review).

Small molecules can activate membrane bound receptors to elicit cellular responses and approximately 80% of all such responses are mediated through membranes. Solid state nuclear magnetic resonance (NMR) methods have been developed for the resolution of specifically labelled ligands, designed to report back structural, dynamic and electronic details of the ligand whilst at its site of action. In particular, ion channel blockers, drugs, inhibitors, prosthetic groups and solutes have been studied when at their target site in functionally competent membranes. A blocker of the channel in the anion transporter of erythrocytes (AE1) has been studied to show that considerable motional freedom within the channel site occurs. The activating agonist of the ligand gated ion channel, the nicotinic acetylcholine receptor, is constrained at its site of action and binds through a cation-pi interaction as revealed in the NMR spectra. The footprint for the inhibitor binding site of the digitalis receptor, the Na(+)/K(+)-ATPase has been resolved as well as the molecular conformation of digitalis showing a bent structure whilst at its site of action. For the gastric proton pump, however, a planar conformation is observed for a reversible substituted imidazopyridine. In all cases not only the structure, but also some indications about the electronic interactions of ligand and target have been resolved using these approaches.

Efficient, long-term transgene expression in Xenopus laevis dermal melanophores.

Xenopus laevis dermal melanophores provide an excellent model system for the investigation of complex cellular processes. Specifically, the expression of exogenous genes in Xenopus melanophores is the basis of recombinant bioassays for the study of receptor-ligand interactions. However, due to their slow rate of cell division and to the relatively low efficiency of current transfection protocols, long-term expression of exogenous genes and the generation of stable melanophore cell lines remains problematic. In this report we demonstrate the efficient, long-term expression of two exogenous proteins, the enhanced green fluorescent protein (EGFP) and the human CD4 (hCD4) cell surface receptor, following stable introduction into Xenopus melanophores via an HIV-1 based vector. Transduction of melanophores with the EGFP expression vector resulted in up to 80% EGFP+ cells. After 1 year in continuous culture in the absence of antibiotic selection, more than 60% of the cells remained EGFP+. Furthermore, we demonstrate the expression of hCD4 melanophores for over 9 months in continuous culture in the absence of antibiotic selection. Our results indicate that lentivirus vectors provide an efficient means of introducing genetic information into Xenopus melanophores, resulting in sustained levels of gene expression. The significance of this gene transfer system for the study of cellular signal transduction pathways is discussed.

Detection and molecular mass determination of an HIV replication-enhancing female genital tract factor using a blot bioassay.

We previously reported that cervicovaginal lavages (CVL) contain a factor that enhances the replication of human immunodeficiency virus (HIV) by increasing virus transcription in T cells and monocytoid cells. This factor was named the HIV-inducing factor (HIF). To determine the molecular mass of HIF, we adapted a blot technique that involves nonreducing SDS-PAGE of CVL samples and electrophoretic transfer onto nitrocellulose paper followed by incubation of paper slices with HIV-infected monocytoid U1 cells. The slices with HIF bioactivity were detected by increased HIV production and measured by an HIV core protein (p24) ELISA. We refer to this technique as the "BioBlot" assay. The BioBlot assay successfully detected bioactivity of HIF anchored onto nitrocellulose and determined that HIF has a molecular mass of about 14 kDa. Paper slices with HIF-negative CVL samples as well as nitrocellulose paper samples without CVL did not enhance HIV production. This finding suggested that SDS-PAGE and nitrocellulose binding do not functionally alter the bioactive domain(s) of HIF structure. In addition to the detection of HIF bioactivity anchored to nitrocellulose and HIF molecular mass determination, the BioBlot technique offers an alternative, rapid method for other applications. These include the study of receptor-ligand interactions of mucosal proteins, direct bioactivity testing and molecular mass determination of secretory substances.