Ligand-receptor Binding Interactions Research Articles

In silico Identification and Optimization of Natural Inhibitors for Drug Target Sites in Cryptosporidium parvum: A Review

Cryptosporidium parvum is the most common enteric protozoan pathogens affecting humans worldwide. Currently approved drugs to treat cryptosporidiosis are ineffective and no vaccines exist against C. parvum. Here, We docked benzoxazole derivatives collected from literature with Cryptosporidium parvum inosine 5′-monophosphate dehydrogenase using AutoDock4.2 tool, which resulted in energy-based descriptors such as Binding Energy, Intermolecular Energy, Internal Energy, Torsional Energy, vdW + Hbond + desolv Energy and electrostatic energy. Molecular dynamics (MD) simulation studies were performed through the NAMD graphical user interface embedded in visual molecular dynamics. After that, we have built quantitative structure activity relationship (QSAR) model using energy-based descriptors yielding correlation coefficient r2 of 0.7948. To assess the predictive performance of QSAR model, different cross-validation procedures were adopted. Our results suggests that ligand-receptor binding interactions for inosine 5′-monophosphate dehydrogenase employing QSAR modeling seems to be a promising approach to design more potent inosine 5′-monophosphate dehydrogenase inhibitors prior to their synthesis.

Analysis of protein ligand-receptor binding by photoaffinity cross-linking.

Photoaffinity cross-linking is a rapidly developing technology for studying biomolecular interactions, including protein ligand-receptor binding. This technology provides detailed binding information including receptor contact sites, active conformation of receptor-ligand complexes, global binding surfaces, and binding modes. Advancements in genetic technology have enabled non-natural photoactive amino acid derivatives to be incorporated into designer or target proteins, providing a host of new opportunities for manufacturing protein photo-probes while bypassing the traditional peptide or small protein limits of classical chemical synthesis. This unit provides several protocols for performing basic photoaffinity cross-linking and related analyses for applications in ligand-receptor binding and protein-protein interactions.

Identification of Ellagic acid analogues as potent inhibitor of protein Kinase CK2:A chemopreventive role in oral Cancer.

Over expression of Protein kinase (CK2) suppresses apoptosis induced by a variety of agents, whereas down-regulation of CK2 sensitizes cells to induction of apoptosis. In this study, we have built quantitative structure activity relationship (QSAR) models, which were trained and tested on experimentally verified 38 enzyme׳s inhibitors having inhibitory value IC50 in µM. These inhibitors were docked at the active site of CK2 (PDB id: 2ZJW) using AutoDock software, which resulted in energy-based descriptors such as binding energy, intermol energy, torsional energy, internal energy and docking energy. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using energy-based descriptors yielding correlation coefficient r2 of 0.4645. To assess the predictive performance of QSAR models, different cross-validation procedures were adopted. Our results suggests that ligand-receptor binding interactions for CK2 employing QSAR modeling seems to be a promising approach for prediction of IC50 value of a new ligand molecule against CK2.Further, twenty analogues of ellagic acid were docked with CK2 structure. After docking, two compounds CID 46229200 and CID 10003463 had lower docking energy even lower than standard control Ellagic acid with CK2 was selected as potent candidate drugs for Oral cancer. The biological activity of two compounds in terms of IC50 was predicted based on QSAR model, which could be used as a guideline for anticancerous activity of compounds before their synthesis.

English

In this work, 3D model of D2 dopamine receptor was determined by comparative homology modeling program MODELLER. The computed model's energy was minimized and validated using PROCHECK and Errat tool to obtain a stable model structure and was submitted in Protein Model Database (PMDB-ID: PM0079251). Stable model was used for molecular docking against Risperidone and their 15 derivatives using AutoDock 4.2, which resulted in energy-based descriptors such as Binding Energy, Ligand Efficiency, Inhib Constant, Intermol energy, vdW + Hbond + desolv Energy, Electrostatic Energy, Total Internal Energy and Torsional Energy. After that, we have built quantitative structure activity relationship (QSAR) model, which was trained and tested on Risperidone and their 15 derivatives having activity value pKi in µM. For QSAR modeling, Multiple Linear Regression model was engendered using energy-based descriptors yielding correlation coefficient r2 of 0.513. To assess the predictive performance of QSAR models, different cross-validation procedures were adopted. Our results suggests that ligand-receptor binding interactions for D2 employing QSAR modeling seems to be a promising approach for prediction of pKi value of novel antagonists against D2 receptor.

Structure-Based Virtual Screening of Compound Library for Anti-Estrogen Breast Cancer Candidates

We reported a structure-based virtual screening of acompound library derived from 3-acyl-5-hydroxybenzofurans to develop potentialdrugs for treating breast cancer. A library of 160,000 compounds was generatedand screened based on the G-score between ligands and receptor ERα. The topstructures were further analyzed to evaluate the receptor-ligand bindinginteractions. By comparing the binding characteristics and docking scoringvalues to the existing ERα analogues, we determined top 200 compounds aspotential drug candidates for breast cancer.

3-Acyl-5-hydroxybenzofuran derivatives as potential anti-estrogen breast cancer agents: A combined experimental and theoretical investigation

We first report the application of 3-acyl-5-hydroxybenzofurans as a scaffold to develop potential drugs for breast cancer. Seven novel derivative compounds were synthesized by using a microwave-assisted synthesis method. Those compounds exhibited different antiproliferation against human breast cancer MCF-7 cells, with the best activity of IC50=43.08μM for compound 1. A Quantum Mechanics Polarized Ligand Docking (QPLD) study was carried out to investigate the binding interactions between these compounds and estrogen receptor alpha (ERα). The simulation results showed that the trend of receptor–ligand binding interactions was same as that of their antiproliferative activities. A detailed analysis indicated that compound 1 possesses the highest Van der Waals and hydrogen bond interactions compared to the other six compounds and better inhibitors are achievable by enhancing the hydrogen bond interactions. Based on these results, we addressed that 3-acyl-5-hydroxybenzofuran is an attractive scaffold for designing drugs against breast cancer.

Metabolite profiling and biological activities of bioactive compounds produced by Chrysosporium lobatum strain BK-3 isolated from Kaziranga National Park, Assam, India

In an ongoing survey for bioactive potential of microorganisms from different biosphere zones of India, a new Chrysosporium lobatum strain BK-3 was isolated from soil sample collected from a biodiversity hotspot, Kaziranga National Park, Assam, India. Bioactivity-guided purification resulted in the isolation of two bioactive compounds whose chemical structures were elucidated by 1H and 13C Nuclear Magnetic Resonance (NMR), 2D-NMR, Fourier Transform Infra-red (FT-IR) and mass spectroscopic techniques, and were identified as α, β-dehydrocurvularin and curvularin. Only curvularin exhibited 80% acetylcholinesterase (AChE) inhibitory activity. Detailed ligand receptor binding interactions were studied for curvularin by molecular docking studies. Further, both curvularin and α, β-dehydrocurvularin had similar level of cytotoxicity against different human tumour cell lines like A549, HeLa, MDA-MB-231 and MCF-7, while α, β-dehydrocurvularin was active against COLO 205 with a IC50 of 7.9 μM, but curvularin was inactive. α, β-Dehydrocurvularin also showed good superoxide anion scavenging activity with an EC50 value of 16.71 μg ml-1. Hence, both these compounds exhibited differences in bioactive profiles and this was probably associated with their minor structural differences. This is a first report on bioactive compounds exhibiting AChE inhibitory, cytotoxicity and antioxidant activities from Chrysosporium lobatum strain BK-3.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-2-122) contains supplementary material, which is available to authorized users.

Implementation of a genetically tuned neural platform in optimizing fluorescence from receptor-ligand binding interactions on microchips.

This paper describes the use of a genetically tuned neural network platform to optimize the fluorescence realized upon binding 5-carboxyfluorescein-D-Ala-D-Ala-D-Ala (5-FAM-(D-Ala)(3) ) (1) to the antibiotic teicoplanin from Actinoplanes teichomyceticus electrostatically attached to a microfluidic channel originally modified with 3-aminopropyltriethoxysilane. Here, three parameters: (i) the length of time teicoplanin was in the microchannel; (ii) the length of time 1 was in the microchannel, thereby, in equilibrium with teicoplanin, and; (iii) the amount of time buffer was flushed through the microchannel to wash out any unbound 1 remaining in the channel, are examined at a constant concentration of 1, with neural network methodology applied to optimize fluorescence. Optimal neural structure provided a best fit model, both for the training set (r(2) = 0.985) and testing set (r(2) = 0.967) data. Simulated results were experimentally validated demonstrating efficiency of the neural network approach and proved superior to the use of multiple linear regression and neural networks using standard back propagation.

Trinuclear ruthenium clusters as bivalent electrochemical probes for ligand-receptor binding interactions.

Despite their popularity, electrochemical biosensors often suffer from low sensitivity. One possible approach to overcome low sensitivity in protein biosensors is to utilize multivalent ligand-receptor interactions. Controlling the spatial arrangement of ligands on surfaces is another crucial aspect of electrochemical biosensor design. We have synthesized and characterized five biotinylated trinuclear ruthenium clusters as potential new biosensor platforms: [Ru(3)O(OAc)(6)CO(4-BMP)(py)](0) (3), [Ru(3)O(OAc)(6)CO(4-BMP)(2)](0) (4), [Ru(3)O(OAc)(6)L(4-BMP)(py)](+) (8), [Ru(3)O(OAc)(6)L(4-BMP)(2)](+) (9), and [Ru(3)O(OAc)(6)L(py)(2)](+) (10) (OAc = acetate, 4-BMP = biotin aminomethylpyridine, py = pyridine, L = pyC16SH). HABA/avidin assays and isothermal titration calorimetry were used to evaluate the avidin binding properties of 3 and 4. The binding constants were found to range from (6.5-8.0) × 10(6) M(-1). Intermolecular protein binding of 4 in solution was determined by native gel electrophoresis. QM, MM, and MD calculations show the capability for the bivalent cluster, 4, to intramolecularly bind to avidin. Electrochemical measurements in solution of 3a and 4a show shifts in E(1/2) of -58 and -53 mV in the presence of avidin, respectively. Self-assembled monolayers formed with 8-10 were investigated as a model biosensor system. Diluent/cluster ratio and composition were found to have a significant effect on the ability of avidin to adequately bind to the cluster. Complexes 8 and 10 showed negligible changes in E(1/2), while complex 9 showed a shift in E(1/2) of -43 mV upon avidin addition. These results suggest that multivalent interactions can have a positive impact on the sensitivity of electrochemical protein biosensors.

Structure–Activity Relationships of GHRP-6 Azapeptide Ligands of the CD36 Scavenger Receptor by Solid-Phase Submonomer Azapeptide Synthesis

The cluster of differentiation 36 (CD36) class B scavenger receptor binds a variety of biologically endogenous ligands in addition to synthetic peptides (i.e., growth hormone-releasing peptides, GHRPs), which modulate biological function related to anti-angiogenic and anti-atherosclerotic activities. Affinity labeling had previously shown that GHRP-6 analogues such as hexarelin, [2-Me-W(2)]GHRP-6 (1), bind to the lysine-rich domain of the CD36 receptor. Moreover, the azapeptide analogue [aza-F(4)]GHRP-6, 2, exhibited a characteristic β-turn conformation as described by CD and NMR spectroscopy and a slightly higher CD36 binding affinity relative to hexarelin (1.34 and 2.37 μM, respectively), suggesting receptor binding was mediated by the conformation and the aromatic residues of these peptide sequences. Ligand-receptor binding interactions were thus explored using azapeptides to examine influences of side-chain diversity and backbone conformation. In particular, considering that aromatic cation interactions may contribute to binding affinity, we have explored the potential of introducing salt bridges to furnish GHRP-6 azapeptide ligands of the CD36 receptor. Fifteen aza-glutamic acid analogues related to 2 were prepared by submonomer solid-phase synthesis. The azapeptide side chains were installed by novel approaches featuring alkylation of resin-bound semicarbazone with Michael acceptors and activated allylic acetates in the presence of phosphazene base (BTPP). Moreover, certain Michael adducts underwent intramolecular cyclization during semicarbazone deprotection, leading to novel pyrrazoline and aza-pyroglutamate N-terminal residues. Structural studies indicated that contingent on sequence the [aza-Glu]GHRP-6 analogues exhibited CD spectra characteristic of random coil, polyproline type II and β-turn secondary structures in aqueous media. In covalent competition binding studies with the GHRP-6 prototype hexarelin bearing a radiotracer, certain [aza-Glu]GHRP-6 azapeptides retained relatively high (2-27 μM) affinity for the CD36 scavenger receptor.

KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials.

BackgroundIdentification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present in bacteria, however absent in mammals. This pathway is vital for bacteria due to its critical role in cell wall biosynthesis. One of the essential enzymes of this pathway is dihydrodipicolinate synthase (DHDPS), considered to be crucial for the bacterial survival. In view of its importance, the development and prediction of potent inhibitors against DHDPS may be valuable to design effective drugs against bacteria, in general.ResultsThis paper describes a methodology for predicting novel/potent inhibitors against DHDPS. Here, quantitative structure activity relationship (QSAR) models were trained and tested on experimentally verified 23 enzyme's inhibitors having inhibitory value (Ki) in the range of 0.005-22(mM). These inhibitors were docked at the active site of DHDPS (1YXD) using AutoDock software, which resulted in 11 energy-based descriptors. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using best four energy-based descriptors yielding correlation values R/q2 of 0.82/0.67 and MAE of 2.43. Additionally, Support Vector Machine (SVM) based model was developed with three crucial descriptors selected using F-stepping remove-one approach, which enhanced the performance by attaining R/q2 values of 0.93/0.80 and MAE of 1.89. To validate the performance of QSAR models, external cross-validation procedure was adopted which accomplished high training/testing correlation values (q2/r2) in the range of 0.78-0.83/0.93-0.95.ConclusionsOur results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed http://crdd.osdd.net/raghava/kidoq, which allows the prediction of Ki value of a new ligand molecule against DHDPS.

3D Pharmacophore, hierarchical methods, and 5-HT4 receptor binding data

5-Hydroxytryptamine subtype-4 (5-HT4) receptors have stimulated considerable interest amongst scientists and clinicians owing to their importance in neurophysiology and potential as therapeutic targets. A comparative analysis of hierarchical methods applied to data from one thousand 5-HT4 receptor–ligand binding interactions was carried out. The chemical structures were described as chemical and pharmacophore fingerprints. The definitions of indices, related to the quality of the hierarchies in being able to distinguish between active and inactive compounds, revealed two interesting hierarchies with the Unity (1 active cluster) and pharmacophore fingerprints (4 active clusters). The results of this study also showed the importance of correct choice of metrics as well as the effectiveness of a new alternative of the Ward clustering algorithm named Energy (Minimum E-Distance method). In parallel, the relationship between these classifications and a previously defined 3D 5-HT4 antagonist pharmacophore was established.

Structural Manipulation of Eicosanoid Receptors and Cellular Signaling

Eicosanoids are lipid mediators derived from the metabolism of arachidonic acid. These agents are locally released and activate different cell membrane receptors, and the latter are part of the G-protein coupled receptor family. While activation of eicosanoid receptors is associated with a wide variety of actions, there is limited information concerning the structural components of the eicosanoid receptors. To date, our understanding of the eicosanoid ligand-receptor binding interaction has been based on the rhodopsin template model. While receptors in the same family do share a common architecture, there are amino acid residues in the membrane binding pocket that play a key role in ligand recognition as well as the diversity observed in the cellular signaling. In order to understand the eicosanoid receptor binding interaction, attention must be focused on both the nature of the endogenous ligands as well as the template G-protein model that has been proposed. The data derived from chemical alterations in the endogenous ligands, together with the mutagenesis studies involving the structural modifications of the eicosanoid receptors, have suggested a working model of the eicosanoid receptors. However, the data also document various nuances in the receptor structure associated with ligand binding as well as a number of differences that will require further investigation.

Nanomechanics: Opening new frontiers in bio analyses and diagnostics

Micro-fabricated silicon cantilevers arrays offer a novel label-free approach where ligand-receptor binding interactions occurring on the sensor generate nanomechanical signals like bending or a change in mass that is optically detected in-situ.We report the detection of multiple unlabelled biomolecules simultaneously down to picomolar concentrations within minutes. Differential measurements including reference cantilevers on an array of eight sensors enables sequence-specifically detection of unlabelled DNA and is suitable to detect specific gene fragments within a complete genome (gene fishing). Expression of detection of inducible genes as well as the ultimate challenge: the detection of total RNA fragments in a unspecific back ground will be shown.Ligand-receptor binding interactions, such as antigen recognition will be presented. Antibody activated cantilevers with sFv (single chain fragments) which bind to the indicator proteins show a significant improved sensitivity which is comparable with SPR (Surface Plasmon Resonance). In addition this technology offers a brought variety of receptor molecules application such as e.g. membrane protein recognition, micro-organism detection, enantiomeric separation.New coating procedures, enlargement of the active surface area by dendritic molecules as well as improvement of the receptor-cantilever chemical bond will be presented.This new findings may lead to a novel individual diagnostic assay in a combined label-free GENOMIC and PROTEOMIC biomarker sensor (COMBIOSENS).

Transport Features, Reaction Kinetics and Receptor Biomechanics Controlling Selectin and Integrin Mediated Cell Adhesion

The distinct and overlapping roles of adhesion molecules belonging to the selectin and integrin families control the rate of leukocyte adhesion to stimulated vascular endothelial cells under hydrodynamic shear flow. Crystal structures have appeared for some of these interactions which complement molecular biology experiments, and clarify the molecular mechanism of the receptor-ligand binding interactions. Binding affinity data have also appeared using surface plasmon resonance and single-molecule biophysics experiments. These studies confirm and extend the predictions of previous experiments carried out in parallel-plate flow chambers, and cone and plate viscometers. This review discusses the current state of understanding on how molecular bond formation rates coupled with cellular and hydrodynamic features regulate leukocyte binding to endothelial cells.

Fluorescence-based array biosensors for detection of biohazards.

Total internal reflection fluorescence (TIRF) is a process whereby fluorophores that are either attached to or are in close proximity with the surface of a waveguide are selectively excited via an evanescent wave. Planar waveguides provide the possibility of immobilizing multiple capture biomolecules onto a single surface and therefore, offer the exciting prospect of multi-analyte detection. The production of arrays and the results of various groups which use TIRF to interrogate such surfaces is reviewed, along with a look at how far the field has advanced toward the production of an automated, portable, multi-analyte array biosensor for real-time biohazard detection. In particular, a miniaturized, fully automated, stand-alone array biosensor developed at the Naval Research Laboratory is reported that monitors interactions between binding partners either as the final image or in real-time. A variety of analytes including toxins, bacteria and viruses have been detected both in buffer and complex matrices, such as blood and soil suspensions, with comparable detection limits. A number of developments have led to a TIRF array biosensor weighing only 5.5 kg which is automated for environmental, clinical and food monitoring or for detection of bioterrorist agents.

Medetomidine analogs as selective agonists for the human α 2-adrenoceptors

α 2-Adrenoceptor (AR) agonists have therapeutic applications in a variety of diseases. Medetomidine, an α 2-AR agonist, belongs to 4-substituted imidazole class of compounds and is highly selective for the α 2-AR. The benzylic methyl group of medetomidine and naphthalene imidazole was proposed to interact with rat brain α 2-ARs via a methyl binding pocket in a manner analogous to its presence in α-methyl norepinephrine. A series of derivatives containing hydrophilic and hydrophobic substituents, as well as chiral and conformationally rigid analogs were used. In current binding and functional studies using human α 2-AR subtypes expressed in Chinese hamster ovary cells, optimal interactions were observed with the presence of the methyl group on the benzylic carbon atom of naphthyl imidazole. Data obtained with various analogs have demonstrated that size, electronegativity, lipophilicity, chirality and conformational flexibility of the substituents at the carbon bridge of naphthyl imidazole are important factors for interaction of the imidazole class of ligands with these α 2-AR subtypes. Taken collectively, the results obtained support the existence of the methyl binding pocket for optimal ligand receptor binding interactions in human α 2-AR subtypes. Further, the results also suggest that, additional modifications of medetomidine and naphthyl methyl imidazole at the benzylic carbon atom, and/or on the aromatic and imidazole ring systems could provide insights into the chemical requirements for optimizing α 2-AR subtype selectivity. This could eventually lead to the discovery of promising compounds for the evaluation of the physiological importance of the three α 2-AR subtypes.

Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array.

We report a microarray of cantilevers to detect multiple unlabeled biomolecules simultaneously at nanomolar concentrations within minutes. Ligand-receptor binding interactions such as DNA hybridization or protein recognition occurring on microfabricated silicon cantilevers generate nanomechanical bending, which is detected optically in situ. Differential measurements including reference cantilevers on an array of eight sensors can sequence-specifically detect unlabeled DNA targets in 80-fold excess of nonmatching DNA as a background and discriminate 3' and 5' overhangs. Our experiments suggest that the nanomechanical motion originates from predominantly steric hindrance effects and depends on the concentration of DNA molecules in solution. We show that cantilever arrays can be used to investigate the thermodynamics of biomolecular interactions mechanically, and we have found that the specificity of the reaction on a cantilever is consistent with solution data. Hence cantilever arrays permit multiple binding assays in parallel and can detect femtomoles of DNA on the cantilever at a DNA concentration in solution of 75 nM.

Allosteric modulation of muscarinic receptor signaling: alcuronium-induced conversion of pilocarpine from an agonist into an antagonist.

Previous studies on allosteric interactions at muscarinic receptors have often focused on ligand-receptor binding interactions, because ligand binding seemed to reflect functional consequences. The prototypal allosteric agent alcuronium is known to bind with similar affinity to the M(2) subtype of muscarinic acetylcholine receptors whether or not the receptors are occupied by the agonist pilocarpine. To determine allosteric modulation of receptor signaling by alcuronium, the effects of pilocarpine were measured in contracting guinea pig left atria and on G-protein coupling in M(2)-transfected Chinese hamster ovary (CHO) cell membranes. Alcuronium dose-dependently suppressed pilocarpine-induced reduction of isometric contraction force in atria (pIC(50, Alc) = 5.63) without any effect on the EC(50) of pilocarpine, consistent with an allosteric mechanism. In contrast, alcuronium shifted the concentration-effect curve of the agonist oxotremorine M to the right without affecting the maximal effect, in a formally competitive manner (pK(A, Alc) = 5.54). If pilocarpine remained receptor bound in the presence of alcuronium, this indicates that pilocarpine can no longer act as an agonist. In support of this hypothesis, pilocarpine acted as a competitive antagonist against oxotremorine M in the presence of 10 microM alcuronium. Measuring guanosine 5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPgammaS) binding in CHO-M(2) membranes yielded similar results. Alcuronium suppressed pilocarpine-induced stimulation of [(35)S]GTPgammaS binding (pIC(50, Alc) = 5.47) without shift in EC(50), whereas it competitively shifted the response to oxotremorine M (pK(A, Alc) = 5.97). [(3)H]Oxotremorine M binding data corresponded with the functional findings. In conclusion, alcuronium converted the agonist pilocarpine into an antagonist-a novel type of functional allosteric interaction.

A possible molecular mechanism for the interaction of defensin with the sensory neuron membrane.

A local membrane potential clamping method was used to study the effects of defensin NP-1 on the membranes of rat spinal ganglion neurons. NP-1 led to decreases in the effective charge for the activation gating system. This process depended on the NP-1 concentration. Use of the Hill equation showed that Kd was 2.10(-12) M and the Hill coefficient was 0.9. The structure of the defensin molecule was optimized using quantum chemical calculations based on a molecular mechanics method. The results obtained from these calculations suggested that a single hydroxyl group directed towards the outer part of thedefensin molecule and forming the carboxyl group of amino acid Glu14 could form a hydrogen bond with the active center of the membrane receptor. This explains the experimentally observed 1:1 stoichiometry of the ligand-receptor binding interaction between the defensin and the sensory neuron membrane.