Ligand-receptor Binding Interactions Research Articles

Two-point immobilization of M3 muscarinic receptor: a method for recognizing receptor antagonists in natural products

In the investigation of active ingredients from natural products, current technologies relying on drug–target affinity recognition analysis face significant challenges. This is primarily due to their limited specificity and inability to provide downstream pharmacodynamic information, such as agonistic or antagonistic activity. In this study, a two-point method was developed by immobilizing M3 acetylcholine receptor (M3R) through the combination of the conformation-specific peptide BJ-PRO-13a and the HaloTag trap system. We systematically assessed the specificity of the immobilized M3R using known M3R antagonists (pirenzepine and atropine) and agonists (cevimeline and pilocarpine). By frontal analysis and nonlinear chromatography, the performance of immobilized M3R was evaluated in terms of binding kinetics and thermodynamics of four drugs to the immobilized M3R. Additionally, we successfully identified two M3R antagonists within an extract from Daturae Flos (DF), specifically hyoscyamine and scopolamine. Our findings demonstrate that this immobilization method effectively captures receptor-ligand binding interactions and can discern receptor agonists from antagonists. This innovation enhances the efficiency of receptor chromatography to determine binding-affinity in the development of new drugs, offering promise for the screening and characterization of active compounds, particularly within complex natural products.

Notch Signaling Is Required for Extramedullary Hematopoiesis in the Adult Liver

During embryonic development, hematopoietic stem cells (HSC) in the fetal liver undergo expansion and self-renewal. Fetal HSCs migrate to the bone marrow (BM) niche towards birth and remain there during adulthood. Extramedullary hematopoiesis (EMH), or hematopoiesis outside of the BM, predominantly occurs in the fetal liver or when the adult BM niche ceases to be a site for functional hematopoiesis. The mechanism by which the adult liver becomes reactivated as a site of EMH for itinerant HSCs is unknown. Our project is investigating EMH in the adult liver by inducing acute hemolytic anemia in adult mice that induces egress and homing of hematopoietic progenitors to the liver and spleen. Our work demonstrates that long-term HSCs isolated from the portal vein in the adult liver can serially reconstitute lethally irradiated mice. Thus, the adult liver serves as a potential reservoir for long-term, functional HSCs in the presence of a damaged BM niche. In pursuit of a mechanism, we focused on Notch-signaling which is an evolutionarily conserved pathway that has been shown to play a critical role in HSC emergence and fetal liver development. When comparing WT liver donors to Notch-deficient (Notch1 +/ΔTAD) or Notch knockout (Notch1 ffVavCre +) liver donors, hematopoietic transplants reveal that Notch mutant progenitors fail to efficiently reconstitute irradiated recipients. Using an HSC-specific a-catulin-GFPmouse model, we are able to track the expression of GFP + liver-originating HSCs after hematopoietic reconstitution. We show that mice reconstituted by EMH-activated a-catulin-GFP liver HSCs are able to provide long-term reconstitution in lethally irradiated recipients and resume residence in the bone marrow niche of recipients. Additionally, we see distinct localization of GFP + HSCs localized near sinusoids throughout the EMH liver niche using whole-mount imaging. We have validated receptor-ligand binding interactions of the Notch1 receptor with ligand-expressing hematopoietic cells in the adult liver. Using intracellular flow cytometry after EMH in the adult liver, we see a 3-fold increase in mean fluorescent intensity of GATA2 in HSPCs (hematopoietic stem cell progenitors) when compared to our bone marrow and isotype control mice. We demonstrate that Notch-driven GATA2 expression is a crucial regulator of self-renewal and functional maintenance of stemness during EMH of HSCs in the adult liver. Our findings reveal a developmentally conserved Notch signaling mechanism is reactivated in the adult liver to retain the functional potential and maintenance of HSCs as they adapt to inhospitable conditions in the bone marrow niche.

MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories.

Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.

Synthesis, characterization, molecular docking studies, and in vitro elucidation of protein aggregation inhibition potential of 3β-acetoxy steroidal pyrazolines

Protein misfolding and amyloid fibril deposition may lead to several neurodegenerative disorders like Alzheimer's, Parkinson's, Huntington's, and similar amyloid polyneuropathies. Inhibition of fibril formation and disaggregation of mature fibrils by some chemical compounds could be a therapeutic approach toward such chronic diseases. In this study, we synthesized a series of novel steroidal pyrazolines and tested the effects of the series on the in vitro inhibition of human lysozyme aggregation. The effect of synthesized steroidal compounds on the kinetics of protein aggregation inhibition was elucidated by Tryptophan (Trp), 8-anilino-1-naphthalenesulfonic acid (ANS), and Congo red (CR) spectral analysis. Further, we examined that the ring closure reaction in the later step produced a mixture of two steroidal pyrazoline epimers that could only be separated in their acetylated form. The (5’S)-3β-acetoxy steroidal pyrazolines (5a-i) were found as the major product and their structures were examined using NMR techniques. The efficacy of various acid catalysts to catalyze the condensation reaction was also evaluated to obtain better yield in lesser time. In addition, molecular docking studies were also performed to understand the receptor-ligand binding interactions.

Purpurin ameliorates alcohol-induced hepatotoxicity by reducing ROS generation and promoting Nrf2 expression

Introduction and aimPurpurin, a naturally occurring anthraquinone isolated from the roots of Rubia cordifolia, exhibits anti-cancer, anti-genotoxic, anti-microbial, neuromodulatory and photodynamic activity. However, purpurin's in vivo and in vitro antioxidant mechanism remains unexplored. The present study explores the anti-oxidative mechanism of purpurin under the influence of alcohol using in vivo and in vitro test systems. MethodsMice hepatocytes and alcohol-induced liver toxicity model were used to evaluate the effect of purpurin. The non-enzymatic and enzymatic oxidative stress markers were estimated by the colorimetric method. The reactive oxygen species (ROS) were quantified in mitochondria and cells using flow cytometer. Real-time PCR and western blotting were used to quantify cytochrome 450 subtype 2E1 (CYP2E1) and Nrf2 expression in the liver tissue of mice. In silico studies were performed through receptor-ligand binding interaction. Key findingsPurpurin effectively reduced total cellular and mitochondrial ROS in primary hepatocytes and WRL-68 cells. It prevented alcohol-induced ROS-dependent biochemical and cellular insults observed by analysing the serum glutamic pyruvic transaminase (SGPT), glutamic-oxaloacetic transaminase (SGOT) levels and CYP2E1 expression in liver tissue of alcohol-administered mice. Moreover, it also restored the activity of antioxidant enzymes. Its antioxidant effect was established by glutathione and ROS-dependent mechanisms using buthionine sulfoximine and N-acetyl cysteine. Along with alcohol, purpurin up-regulated Nrf2 expression in hepatocytes. SignificanceThis work confirmed the ameliorative effect of purpurin for alcohol-induced hepatotoxicity by drabbing free radicals and curbing oxidative stress via activation of antioxidant signalling pathways.

The Synthesis and Docking Study of Novel Compounds for Variola Virus

Three novel compounds, namely, 4-amino-5-(2,3,4,5,6-pentahydroxy-1-(4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)hexyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one SG-3, 3-methyl-5-(2,3,4,5,6-pentahydroxy-1-(4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)hexyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one-(2H)-ylamino)butanoic acid SG-4 and 2-(4-oxo-5-(2,3,4,5,6-pentahydroxy-1-(4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)hexyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one-2-phenylacetic acid SG-6 were synthesized from easily available, inexpensive, environmentally friendly starting materials (glucose, amino acid and thiobarbutric acid) and characterized by 1H-NMR, 13C-NMR and mass spectroscopy. the molecular modelling of these compounds was studied in Crystal structure of vaccinia virus thymidylate kinase , for the treatment of variola. Their binding motifs and drug-like properties were investigated. Results show that all compounds confirmed appropriate binding free energies; between –9.71 and –10.11 Kcal/mol . Since the novel molecules have high ligand-receptor binding interactions, they can be a powerful alternative to FDA approved drug Cidofovir.

QSAR modeling and docking analysis of D2 receptor with known olanzapine derivatives.

Dopamine (D2) receptors are known drug targets for various antipsychotics used in Schizophrenia. Therefore, it is of interest to analyze the binding features of D2 receptors with known olanzapine derivatives for further consideration using molecular docking and QSAR analysis. A 2D QSAR model was built using energy-based descriptors generated by docking as independent variable and known Ki value of Olanzapine derivatives with D2 Receptor as dependent variable. QSAR model provided coefficient of determination of r2 of 0.7 in multiple linear regression analysis. The predictive performance of QSAR model was assessed using different cross-validation procedures. Thus, data shows that a ligand-receptor binding interaction for D2 Receptor using a QSAR model is promising approach to design novel and potent inhibitors of D2 Receptor.

Binding of a Brownian nanoparticle to a thermally fluctuating membrane surface.

We investigate the Brownian dynamics of a nanoparticle bound to a thermally undulating elastic membrane. The ligand-functionalized nanoparticle is assumed to interact monovalently with the receptor expressed on the membrane. In order to resolve the nanoparticle transient motion subject to the instantaneous membrane configuration in a consistent manner, we employ a set of coupled Langevin equations that simultaneously incorporate the hydrodynamic effects, ligand-receptor binding interaction, intramembrane elastic forces, and thermal fluctuations. We show that the presence of a deformable, elastic fluid membrane not only affects the dynamics of a bound nanoparticle but also alters the effective binding potential felt by the nanoparticle. In contrast to a nanoparticle bound to a flat surface, the oscillatory characteristics of the nanoparticle velocity autocorrelation function are suppressed and transition to an anticorrelated long-time tail. Moreover, the nanoparticle position fluctuation becomes more coherent with that of the membrane binding site, and the width of the distribution of the nanoparticle distance from the membrane decreases with increasing membrane bending rigidity. By introducing a locally harmonic, bistable potential as an effective potential for the ligand-receptor pair, the rate of nanoparticle transitioning between two bound states is facilitated by membrane undulations as a result of stronger positional variations associated with the nanoparticle.

Exception That Proves the Rule: Investigation of Privileged Stereochemistry in Designing Dopamine D3R Bitopic Agonists.

In this study, starting from our selective D3R agonist FOB02-04A (5), we investigated the chemical space around the linker portion of the molecule via insertion of a hydroxyl substituent and ring-expansion of the trans-cyclopropyl moiety into a trans-cyclohexyl scaffold. Moreover, to further elucidate the importance of the primary pharmacophore stereochemistry in the design of bitopic ligands, we investigated the chiral requirements of (+)-PD128907 ((+)-(4a R ,10b R )-2)) by synthesizing and resolving bitopic analogues in all the cis and trans combinations of its 9-methoxy-3,4,4a,10b-tetrahydro-2H,5H-chromeno[4,3-b][1,4] oxazine scaffold. Despite the lack of success in obtaining new analogues with improved biological profiles, in comparison to our current leads, a "negative" result due to a poor or simply not improved biological profile is fundamental toward better understanding chemical space and optimal stereochemistry for target recognition. Herein, we identified essential structural information to understand the differences between orthosteric and bitopic ligand-receptor binding interactions, discriminate D3R active and inactive states, and assist multitarget receptor recognition. Exploring stereochemical complexity and developing extended D3R SAR from this new library complements previously described SAR and inspires future structural and computational biology investigation. Moreover, the expansion of chemical space characterization for D3R agonism may be utilized in machine learning and artificial intelligence (AI)-based drug design, in the future.

Lipid Bicelle Micropatterning Using Chemical Lift-Off Lithography.

Supported lipid membranes are versatile biomimetic coatings for the chemical functionalization of inorganic surfaces. Developing simple and effective fabrication strategies to form supported lipid membranes with micropatterned geometries is a long-standing challenge. Herein, we demonstrate how the combination of chemical lift-off lithography (CLL) and easily prepared lipid bicelle nanostructures can yield micropatterned, supported lipid membranes on gold surfaces with high pattern resolution, conformal character, and biofunctionality. Using CLL, we functionalized gold surfaces with patterned arrays of hydrophilic and hydrophobic self-assembled monolayers (SAMs). Time-lapse fluorescence microscopy imaging revealed that lipid bicelles adsorbed preferentially onto the hydrophilic SAM regions, while there was negligible lipid adsorption onto the hydrophobic SAM regions. Functional receptors could be embedded within the lipid bicelles, which facilitated selective detection of receptor-ligand binding interactions in a model streptavidin-biotin system. Quartz crystal microbalance-dissipation measurements further identified that lipid bicelles adsorb irreversibly and remain intact on top of the hydrophilic SAM regions. Taken together, our findings indicate that lipid bicelles are useful lipid nanostructures for reproducibly assembling micropatterned, supported lipid membranes with precise pattern fidelity.

Synthesis, Antimicrobial Evaluation and Molecular Docking of Some Potential 2,6-disubstituted 1H-Benzimidazoles; Non-Classical Antifolates.

Dihydrofolate reductase is one of the important enzymes for thymidylate and purine synthesis in micro-organisms. A large number of drugs have been designed to inhibit microbial DHFR but over the period of time, some drugs have developed resistance and cross reactivity towards the enzyme. Over the past few decades, benzimidazoles, triazoles and their derivatives have been grabbing the attention of the synthetic chemists for their wide gamut of antibacterial and antifungal activities targeting microbial protein DHFR. Our goal behind present investigation is to explore benzimidazoles class of drugs as microbial DHFR inhibitors by studying ligand-receptor binding interactions, in vitro enzyme inhibition assay and confirmation of anti-microbial activity against selected pathogenic microorganisms. A library containing thirty novel 2,6-disubstituted 1H-benzimidazoles was synthesized by one pot condensation of o-nitro aniline or 2,4-dinitro aniline with series of aldehydes or acetophenones using Na2S2O4 or SnCl2 respectively and reflux for 5-6hr. Structures of compounds have been confirmed by spectroscopic methods as 1H and 13C NMR, FT-IR and MS. In vitro DHFR inhibition study was performed by using Epoch microplate reader and IC50 of the test compounds was compared with Trimethoprim. In vitro antimicrobial activity was performed against selected clinical pathogens by agar disk diffusion method and MIC (µg/mL) was reported. Moderate to good level of DHFR inhibition was observed with IC50 values in the range of 7-23 µM. Compounds B1, B19, B22, B24 and B30 expressed 1.1 to 1.4 folds more prominent DHFR inhibitory activity as compared to standard Trimethoprim. Remarkable antimicrobial activity was exhibited by B1, B19, B22, B24 and B30. Molecular docking study revealed perfect binding of test ligands with key amino acids of DHFR as Phe31, Ile94, Ile5, Asp27, Gln32 and Phe36. Nature of 1H-benzimidazole substituents at position 2 and 6 had influence over magnitude and type of molecular binding and variation in the biological activity. The present series of 1H-benzimidazoles could be considered promising broad-spectrum antimicrobial candidates that deserve in future for preclinical antimicrobial evaluation and development of newer antimicrobial agents targeting microbial DHFR.

Rutin protects t‑butyl hydroperoxide-induced oxidative impairment via modulating the Nrf2 and iNOS activity

BackgroundRutin (quercetin-3-O-rutinoside), a flavonoid, is predominantly found in the buckwheat, cranberries, mulberry and citrus fruits. It is used as a restorative in the preparation of herbal medicine, multivitamin and known to reduce the fate of heart attack. HypothesisWe aimed to elucidate whether rutin attenuates oxidative stress and its possible mechanism of action in ameliorating the deleterious effect of t-BHP. We also provide evidence that rutin protects the antioxidant status of erythrocytes and liver via Nrf2 and iNOS pathway from oxidative stress. Study Design/MethodHuman erythrocytes and mice liver were used for the evaluation of rutin's effect against t-BHP induced oxidative stress. The non-enzymatic (GSH, MDA, -CO, –SH) and enzymatic stress markers (SOD, CAT, GPx, GR and GST) were estimated by the colorimetric method. The level of Nrf2, iNOS, liver marker enzymes, triglycerides, cholesterol, HDL-cholesterol, albumin, BUN was measured using ELISA kits. Reactive oxygen species (ROS) was quantified using flow cytometry and fluorometry. RT-PCR was used for the quantification of Nrf2 and iNOS expression levels in the liver tissue of mice. In silico studies were done through receptor-ligand binding interaction. ResultsPre-treatment with the rutin ameliorated the toxic effect of t-BHP by modulating the basal level of GSH, -SH, MDA and –CO significantly (p < 0.01) with respect to untreated control. Rutin also protected the erythrocytes against the t-BHP-induced oxidative stress as evidenced by augmented activity of antioxidant enzymes (CAT, SOD, GPX, GR and GST). Furthermore, at the highest tested concentration (16.3 µM), it protected the morphology of the erythrocytes by decreasing the ROS level (p < 0.01). In addition, the lower MEF values of rutin (0.520 ± 0.005) alone or along with t-BHP (0.630 ± 0.021) indicated its non-toxic and protective behavior. The qPCR analyses revealed that t-BHP potently up-regulates the iNOS and down regulate the Nrf2 expression which was ameliorated with rutin treatment in a dose-dependent manner like silymarin. ConclusionOur findings demonstrate that rutin potentiates its beneficial aspect by displaying a profound role in iNOS-Nrf2 signaling pathway. Accordingly, it may be concluded that the dietary factors wherein rutin is an ingredient could be helpful in the maintenance of the intracellular redox-homeostasis and thus may be effective against oxidative stress related secondary complications.

Synthetic Analogues of the Snail Toxin 6-Bromo-2-mercaptotryptamine Dimer (BrMT) Reveal That Lipid Bilayer Perturbation Does Not Underlie Its Modulation of Voltage-Gated Potassium Channels.

Drugs do not act solely by canonical ligand-receptor binding interactions. Amphiphilic drugs partition into membranes, thereby perturbing bulk lipid bilayer properties and possibly altering the function of membrane proteins. Distinguishing membrane perturbation from more direct protein-ligand interactions is an ongoing challenge in chemical biology. Herein, we present one strategy for doing so, using dimeric 6-bromo-2-mercaptotryptamine (BrMT) and synthetic analogues. BrMT is a chemically unstable marine snail toxin that has unique effects on voltage-gated K+ channel proteins, making it an attractive medicinal chemistry lead. BrMT is amphiphilic and perturbs lipid bilayers, raising the question of whether its action against K+ channels is merely a manifestation of membrane perturbation. To determine whether medicinal chemistry approaches to improve BrMT might be viable, we synthesized BrMT and 11 analogues and determined their activities in parallel assays measuring K+ channel activity and lipid bilayer properties. Structure-activity relationships were determined for modulation of the Kv1.4 channel, bilayer partitioning, and bilayer perturbation. Neither membrane partitioning nor bilayer perturbation correlates with K+ channel modulation. We conclude that BrMT's membrane interactions are not critical for its inhibition of Kv1.4 activation. Further, we found that alkyl or ether linkages can replace the chemically labile disulfide bond in the BrMT pharmacophore, and we identified additional regions of the scaffold that are amenable to chemical modification. Our work demonstrates a strategy for determining if drugs act by specific interactions or bilayer-dependent mechanisms, and chemically stable modulators of Kv1 channels are reported.

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1 415 871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. Supplementary data are available at Bioinformatics online.

PEGylated dendrimer-entrapped gold nanoparticles with low immunogenicity for targeted gene delivery.

The high efficiency and specificity of gene therapy are mainly ascribed to the excellent transfection ability of the gene carrier. Non-viral polymer vectors have attracted extensive attention because of their low cytotoxicity and outstanding genetic loading capacity compared with viral vectors. For safe and efficient transfection of nuclear acids, here we report a novel gene delivery system, dendrimer-entrapped gold nanoparticles modified with a folate-conjugated poly (ethylene glycol) (Au DENPs-PEG-FA), possessing superior gene transfection efficiency than that of partially hydrophilic methoxy poly(ethylene glycol) (mPEG)-modified dendrimer-entrapped gold nanoparticles (Au DENPs-mPEG). The prepared Au DENPs-PEG-FA were well characterized, and our data revealed that the vector showed good cytocompatibility. Additionally, the quantification of inflammatory cytokines detected by qRT-PCR showed that the vectors displayed low innate immune response. The efficiency of nucleic acid (encoding enhanced green fluorescent protein (EGFP) and luciferase (Luc) reporter) transfection evaluated via flow cytometry and confocal microscopic imaging suggested that the Au DENPs-PEG-FA were able to transfect nucleic acid into HeLa cells with enhanced transfection efficiency. Furthermore, the existence of FA rendered the Au DENPs with excellent targeting performance via FA receptor-ligand binding interaction. The designed Au DENPs-PEG-FA with low immunogenicity and enhanced gene transfection efficiency may hold a great promise to be a superior vector for gene therapy.

A QSAR model of Olanzapine derivatives as potential inhibitors for 5-HT2A Receptor.

Schizophrenia is a complex, chronic mental disorder, affecting about 21 million people worldwide. It is characterized by symptoms, including distortions in thinking, perception, emotions, disorganized speech, sense of self and behavior. Recently, a numbers of marketed drugs for Schizophrenia are available against dopamine D2 and serotonin 5-HT2A receptors. Here, we docked Olanzapine derivatives (collected from literature) with 5-HT2A Receptor using the program AutoDock 4.2. The docked protein inhibitor complex structure was optimized using molecular dynamics simulation for 5ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1.9.2) and then evaluating the stability of complex structure by calculating RMSD values. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. A quantitative structure activity relationship (QSAR) model was built using energy-based descriptors as independent variable and pKi value as dependent variable of eleven known Olanzapine derivatives with 5-HT2A Receptor, yielding correlation coefficient r2 of 0.63861. The predictive performance of QSAR model was assessed using different crossvalidation procedures. Our results suggest that a ligand-receptor binding interaction for 5-HT2A receptor using a QSAR model is promising approach to design more potent 5-HT2A receptor inhibitors prior to their synthesis.

Brassinolide-like activity of castasterone analogs with varied side chains against rice lamina inclination

Brassinolide (BL) and castasterone (CS) are the representative members of brassinosteroid class of plant steroid hormone having plant growth promoting activity. In this study, eleven CS analogs bearing a variety of side chains were synthesized to determine the effect of the side chain structures on the BL-like activity. The plant hormonal activity was evaluated in a dwarf rice lamina inclination assay, and the potency was determined as the reciprocal logarithm of the 50% effective dose (ED50) from each dose-response curve. The reciprocal logarithm of ED50 (pED50) was decreased dramatically upon deletion of the C-28 methyl group of CS. The introduction of oxygen-containing groups such as hydroxy, methoxy, and ethoxycarbonyl was also unfavorable to the activity. The pED50 was influenced by the geometry of carbon-carbon double bond between C-24 and C-25 (cis and trans), but the introduction of a fluorine atom at the C-25 position of the double bond did not significantly change the activity. The binding free energy (ΔG) was calculated for all ligand–receptor binding interactions using molecular dynamics, resulting that ΔG is linearly correlated with the pED50.

On the validity and errors of the pseudo-first-order kinetics in ligand–receptor binding

The simple bimolecular ligand–receptor binding interaction is often linearized by assuming pseudo-first-order kinetics when one species is present in excess. Here, a phase-plane analysis allows the derivation of a new condition for the validity of pseudo-first-order kinetics that is independent of the initial receptor concentration. The validity of the derived condition is analyzed from two viewpoints. In the first, time courses of the exact and approximate solutions to the ligand–receptor rate equations are compared when all rate constants are known. The second viewpoint assesses the validity through the error induced when the approximate equation is used to estimate kinetic constants from data. Although these two interpretations of validity are often assumed to coincide, we show that they are distinct, and that large errors are possible in estimated kinetic constants, even when the linearized and exact rate equations provide nearly identical solutions.

A QSAR model of benzoxazole derivatives as potential inhibitors for inosine 5`-monophosphate dehydrogenase from Cryptosporidium parvum.

Cryptosporidium parvum is the common enteric protozoan pathogen causing cryptosporidiosis in human. Available drugs to treat cryptosporidiosis are ineffective and there is yet no vaccine against C. parvum. Therefore, it is of interest to design an improved yet effective drug against C. parvum. Here, we docked benzoxazole derivatives (collected from literature) with inosine 5`- monophosphate dehydrogenase (IMPDH) from Cryptosporidium parvum using the program AutoDock 4.2. The docked protein - inhibitor complex structure was optimized using molecular dynamics simulation for 5 ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1.9.2) and then evaluating the stability of complex structure by calculating RMSD values. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. A quantitative structure activity relationship (QSAR) model was built using energy-based descriptors as independent variable and pIC50 value as dependent variable of fifteen known benzoxazole derivatives with C. parvum IMPDH protein, yielding correlation coefficient r2 of 0.7948. The predictive performance of QSAR model was assessed using different cross-validation procedures. Our results suggest that a ligand-receptor binding interaction for inosine 5`-monophosphate dehydrogenase using a QSAR model is promising approach to design more potent inosine 5`-monophosphate dehydrogenase inhibitors prior to their synthesis.

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.