Caffeine Molecular Imprinted Microgel Spheres by Precipitation Polymerization

Imprinted uniform microgel spheres were prepared by precipitation polymerization. Acetonitrile was used as the dilute solvent with MAA as the monomer, EDMA as the crosslinker and caffeine as the print molecule. Comparison of caffeine adsorption on molecular imprinted and blank microgel spheres was made. Langmuir model was used to fit the adsorption data. It was found that the caffeine imprinted microgel spheres show specific binding sites to the target molecules. A binding study of caffeine on imprinted microgel spheres was made by Scatchard analysis; the dissociation constants (K_D) and the maximum binding capacity were K_D= 1.84×10⁻⁴mol/L,Q _max = 16.98 μmol/g for high affinity binding site and K_D=1.33×l0⁻³ mol/L, Q_max=46.84 μmol/g for lower affinity binding site, respectively This microgel spheres can be useful affinity adsorbents in further applications.     

Discovery of a competitive apelin receptor (APJ) antagonist

The apelin receptor (APJ) is a class A G‐protein‐coupled receptor (GPCR) and is a putative target for the treatment of cardiovascular and metabolic diseases. Apelin‐13 (NH₂‐QRPRLSHKGPMPF‐COOH) is a vasoactive peptide and one of the most potent endogenous inotropic agents identified to date. We report the design and discovery of a novel APJ antagonist. By using a bivalent ligand approach, we have designed compounds with two ′affinity′ motifs and a short series of linker groups with different conformational and non‐bonded interaction properties. One of these, cyclo(1–6)CRPRLC‐KH‐cyclo(9–14)CRPRLC is a competitive antagonist at APJ. Radioligand binding in CHO cells transfected with human APJ gave a K_i value of 82 nM , competition binding in human left ventricle gave a K_D value of 3.2 μM , and cAMP accumulation assays in CHO‐K1‐APJ cells gave a K_D value of 1.32 μM .     

A Single Second Shell Amino Acid Determines Affinity and Kinetics of Linagliptin Binding to Type 4 Dipeptidyl Peptidase and Fibroblast Activation Protein

Drugs targeting type 4 dipeptidyl peptidase (DPP-4) are beneficial for glycemic control, whereas fibroblast activation protein alpha (FAP-α) is a potential target for cancer therapies. Unlike other gliptins, linagliptin displays FAP inhibition. We compared biophysical and structural characteristics of linagliptin binding to DPP-4 and FAP to better understand what differentiates linagliptin from other gliptins. Linagliptin exhibited high binding affinity (K_D) and a slow off-rate (k_off) when dissociating from DPP-4 (K_D 6.6 pM; k_off 5.1×10⁻⁵ s⁻¹), and weaker inhibitory potency to FAP (K_D 301 nM; k_off>1 s⁻¹). Co-structures of linagliptin with DPP-4 or FAP were similar except for one second shell amino acid difference: Asp663 (DPP-4) and Ala657 (FAP). pH dependence of enzymatic activities and binding of linagliptin for DPP-4 and FAP are dependent on this single amino acid difference. While linagliptin may not display any anticancer activity at therapeutic doses, our findings may guide future studies for the development of optimized inhibitors.     

Exploring Non‐obvious Hydrophobic Binding Pockets on Protein Surfaces: Increasing Affinities in Peptide–Protein Interactions

A 42‐residue polypeptide conjugated to a small‐molecule organic ligand capable of targeting the phosphorylated side chain of Ser15 was shown to bind glycogen phosphorylase a (GPa) with a K_D value of 280 nm . The replacement of hydrophobic amino acids by Ala reduced affinities, whereas the incorporation of l ‐2‐aminooctanoic acid (Aoc) increased them. Replacing Nle5, Ile9 and Leu12 by Aoc reduced the K_D value from 280 to 27 nm . “Downsizing” the 42‐mer to an undecamer gave rise to an affinity for GPa an order of magnitude lower, but the undecamer in which Nle5, Ile9 and Leu12 were replaced by Aoc showed a K_D value of 550 nm , comparable with that of the parent 42‐mer. The use of Aoc residues offers a convenient route to increased affinity in protein recognition as well as a strategy for the “downsizing” of peptides essentially without loss of affinity. The results show that hydrophobic binding sites can be found on protein surfaces by comparing the affinities of polypeptide conjugates in which Aoc residues replace Nle, Ile, Leu or Phe with those of their unmodified counterparts. Polypeptide conjugates thus provide valuable opportunities for the optimization of peptides and small organic compounds in biotechnology and biomedicine.     

Structure‐Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics

Structure‐based virtual screening using a D₂ receptor homology model was performed to identify dopamine D₂ receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D₂ ligands were identified (47.6 % success rate, among them D₂ receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5‐HT_2A receptors. The affinity (K_i values) of the compounds ranged from 58 nm to about 24 μm . Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D₂ receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D₂ pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20‐fold binding selectivity for the D₂ receptor over the D₃ receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction.     

Copper is a Cofactor of the Formylglycine‐Generating Enzyme

Formylglycine‐generating enzyme (FGE) is an O₂‐utilizing oxidase that converts specific cysteine residues of client proteins to formylglycine. We show that Cu^I is an integral cofactor of this enzyme and binds with high affinity (K_D=of 10^?17 m ) to a pair of active‐site cysteines. These findings establish FGE as a novel type of copper enzyme.     

Synthesis and antimicrobial activity of the Schiff base from polyoxyalkylene‐montmorillonite nanocomposites and aldehydes

Vanillin (4‐hydroxy‐3‐methoxy benzaldehyde) and 5‐formylamino salicylic acid microbicides were reacted with polyoxyalkylene‐montmorillonite (D_230–2000‐MMT) nanocomposites. The microstructure of these Schiff base nanocomposites was characterized by TEM and XRD. D_230–2000‐MMT nanocomposites were prepared by an ion exchange process of sodium montmorillonite (Na‐MMT) and NH₃ ⁺ groups in polyoxyalkylene amine hydrochloride with three different molecular masses of D₂₃₀, D₄₀₀, and D₂₀₀₀. Wide‐angle X‐ray diffraction confirms the intercalation of the polymer between the silicate layers. Electrostatic interaction between the positively charged NH₃ ⁺ groups and the negatively charged surface of MMT was observed. The nanocomposites were tested for antimicrobial activity against the Gram‐negative bacteria (Escherichia coli NCIM 2065), Gram‐positive bacteria (Bacillus subtillus ATCC), and fungi (Candida albicans SC5314 and Cryptococcus neoformans). The D₂₀₀₀‐MMT/vanillin Schiff base nanocomposite strongly inhibited the growth of all microorganisms that can be used in different applications. The amount of loaded polymer and the structure of the nanocomposite play an important role in inhibiting the bacterial and fungal strains. It is found that the Schiff base nanocomposite affect the morphology, oxygen consumption, and the release of cytoplasmic constituents such as potassium (K⁺), sodium (Na⁺), and calcium (Ca²⁺) ions leading to death of the cells. POLYM. COMPOS., 2012. © 2012 Society of Plastics Engineers     

Preparation and mechanical properties of exfoliated mica-polyamide 6 nanocomposites using sericite mica

A new mica/polyamide 6 (PA6) nanocomposite was formed by exfoliation of a mica, potassium sericite (K⁺-SE). The powder sample was separated through an air-classifier into D₅₀:6.0 μm (median particle diameter), D₁₀:3.5 μm, and D₉₀:9.5 μm. The K⁺-SE was modified with a dodecylammonium salt (DDA) by ion exchange at 70 °C for four days. The resulting organically modified SE was melt-kneaded with PA6 in a twin-screw kneader at 260 °C. In order to characterize the nanocomposite morphology, X-ray diffraction and transmission electron microscopy were used. Differential scanning calorimetry and mechanical property measurements were also carried out. The morphology of the nanocomposite revealed mica nanolayers with very high aspect ratios; that is, at levels about two times greater than that of conventional exfoliated clay-polymer nanocomposites. A small amount of organically modified SE with 2.1 mass% silicate was sufficient to improve the flexural properties and heat distortion temperature of the nanocomposite. However, overall mechanical properties were not completely improved, because the shearing stress induced during exfoliation of the silicate layers resulted in inhomogenous dispersion of silicate platelets in the matrix. The present study indicates that three factors, degree of exfoliation, aspect ratio and dispersion homogeneity of silicate platelets, play an important role for the development of high performance nanocomposites.     

Pramipexole Derivatives as Potent and Selective Dopamine D3 Receptor Agonists with Improved Human Microsomal Stability

Herein we report the synthesis and evaluation of a series of new pramipexole derivatives as highly potent and selective agonists of the dopamine‐3 (D₃) receptor. A number of these new compounds bind to the D₃ receptor with sub‐nanomolar affinity and show excellent selectivity (>10 000) for the D₃ receptor over the D₁ and D₂ receptors. For example, compound 23 (N‐(cis‐3‐(2‐(((S)‐2‐amino‐4,5,6,7‐tetrahydrobenzo[d]thiazol‐6‐yl)(propyl)amino)ethyl)‐3‐hydroxycyclobutyl)‐3‐(5‐methyl‐1,2,4‐oxadiazol‐3‐yl)benzamide) binds to the D₃ receptor with a K_i value of 0.53 nM and shows a selectivity of >20 000 over the D₂ and D₁ receptors in the binding assays using a rat brain preparation. It has excellent stability in human liver microsomes. Moreover, in vitro functional assays showed it to be a full agonist for the human D₃ receptor.     

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (K_D=42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3–HSP90 binding was confirmed (K_D=13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.     

Criteria for the affinity of dyes for fibres

An equation was obtained for evaluating the thermodynamic affinity of a disperse dye for a fibre. Quantities Δh _D and K _D , which are functions of the composition of the dye bath, temperature, and state of the fibre material, can characterize the change in the affinity of the dye for the fibre when the dyeing conditions are varied.     

Synthesis of a Series of Structurally Diverse MB327 Derivatives and Their Affinity Characterization at the Nicotinic Acetylcholine Receptor

A novel series of 30 symmetric bispyridinium and related N‐heteroaromatic bisquaternary salts with a propane‐1,3‐diyl linker was synthesized and characterized for their binding affinity at the MB327 binding site of nicotinic acetylcholine receptor (nAChR) from Torpedo californica. Compounds targeting this binding site are of particular interest for research into new antidotes against organophosphate poisoning, as therapeutically active 4‐tert‐butyl‐substituted bispyridinium salt MB327 was previously identified as a nAChR re‐sensitizer. Efficient access to the target compounds was provided by newly developed methods enabling N‐alkylation of sterically hindered or electronically deactivated heterocycles exhibiting a wide variety of functional groups. Determination of binding affinities toward the MB327 binding site at the nAChR, using a recently developed mass spectrometry (MS)‐based Binding Assay, revealed that several compounds reached affinities similar to that of MB327 (pK_i=4.73±0.03). Notably, the newly prepared lipophilic 4‐tert‐butyl‐3‐phenyl‐substituted bispyridinium salt PTM0022 ( 3 h ) was found to have significantly higher binding affinity, with a pK_i value of 5.16±0.07, thus representing considerable progress toward the development of more potent nAChR re‐sensitizers.     

A Scaffold-Hopping Strategy toward the Identification of Inhibitors of Cyclin G Associated Kinase

We recently reported the discovery of isothiazolo[4,3-b]pyridine-based inhibitors of cyclin G associated kinase (GAK) displaying low nanomolar binding affinity for GAK and demonstrating broad-spectrum antiviral activity. To come up with novel core structures that act as GAK inhibitors, a scaffold-hopping approach was applied starting from two different isothiazolo[4,3-b]pyridines. In total, 13 novel 5,6- and 6,6-fused bicyclic heteroaromatic scaffolds were synthesized. Four of them displayed GAK affinity with K_d values in the low micromolar range that can serve as chemical starting points for the discovery of GAK inhibitors based on a different scaffold.     

Development of a High-Affinity Antibody-Binding Peptide for Site-Specific Modification

Immunoglobulin G (IgG)-binding peptides such as 15-IgBP are convenient tools for the site-specific modification of antibodies and the preparation of homogeneous antibody–drug conjugates. A peptide such as 15-IgBP can be selectively crosslinked to the fragment crystallizable region of human IgG in an affinity-dependent manner via the ϵ-amino group of Lys8. Previously, we found that the peptide 15-Lys8Leu has a high affinity (K_d=8.19 nM) due to the presence of the γ-dimethyl group in Leu8. The primary amino group required for the crosslinking to the antibodies has, however, been lost. Here, we report the design and synthesis of a novel unnatural amino acid, 4-(2-aminoethylcarbamoyl)leucine (Aecl), which possesses both the γ-dimethyl fragment and a primary amino group. A peptide containing Aecl8 (15-Lys8Aecl) was synthesized and showed a binding affinity ten times higher (K_d=24.3 nM) than that of 15-IgBP (K_d=267 nM). Fluorescein isothiocyanate (FITC)-labeled 15-Lys8Aecl with an N-hydroxy succinimide ester at the side chain of Aecl8 (FITC-15-Lys8Aecl(OSu)) successfully labeled an antibody (trastuzumab, Herceptin^®) with the fluorophore. This peptide scaffold has both strong binding affinity and crosslinking capability, and could be a useful tool for the selective chemical modification of antibodies with molecules of interest such as drugs.     

Gum Acacia‐cl‐poly(acrylamide)@carbon nitride Nanocomposite Hydrogel for Adsorption of Ciprofloxacin and its Sustained Release in Artificial Ocular Solution

In the present work, a nanocomposite hydrogel is designed consisting of gum acacia, poly(acrylamide) and carbon nitride by facile microwave approach. This nanocomposite hydrogel is sensitive to environmental stimuli which is essential for its application in environmental remediation and as a drug delivery system. The effects of carbon nitride percentage and microwave Watt variation on swelling capacity of gum acacia‐cl‐poly(acrylamide)@carbon nitride (Ga‐cl‐PAM@C₃N₄) nanocomposite hydrogel are analyzed. The structural characterizations are considered by numerous techniques such as FTIR (Fourier transform infra‐red spectroscopy), X‐ray diffraction, transmission electron microscopy, scanning electron microscopy, and elemental mapping. Batch experiment is performed for remediation of ciprofloxacin (CIP) drug from water. Various parameters such as effect of ciprofloxacin doses, Ga‐cl‐PAM@C₃N₄ nanocomposite hydrogel dosage, pH, time and temperature for adsorption of CIP on gum acacia‐cl‐poly(acrylamide)@carbon nitride nanocomposite hydrogel is examined. Maximum adsorption capacity of Ga‐cl‐PAM@C₃N₄ nanocomposite hydrogel observed is 169.49 mg g^?1 at pH 6.4. The drug loading and drug release capacity of Ga‐cl‐PAM@C₃N₄ nanocomposite hydrogel is investigated for ciprofloxacin. Drug release is monitored in artificial ocular solution (pH 8), saline (pH 5.5), acetate buffer (pH 2.2), and distilled water. Maximum drug release is observed in artificial ocular solution.     

Preparation and utilization of microporous molecularly imprinted polymer for sustained release of tetracycline

A polyacrylate tetracycline (TC) selective microporous molecularly imprinted polymer was prepared in three different porogenic solvents (chloroform, acetonitrile, and methanol) via precipitation polymerization, using methacrylic acid monomer, ethylene glycol dimethacrylate crosslinker, and TC as template. In all three solvents this method produced microporous particles in the scale range (200–400 nm), simply, quickly, cleanly, and in good yield. The effect of polarity of porogenic solvents on binding capacity was investigated. The imprinted polymer prepared in chloroform gave much higher binding capacity (K_D = 198.6) for TC than the polymers prepared in acetonitrile (K_D = 133.2) or methanol (K_D = 104.7). The selectivity of imprinted polymers was evaluated by rebinding other structurally similar compounds. The results clearly indicated that the imprinted acrylate polymer exhibits an excellent selectivity toward TC, and has better ability to control the release of TC than the non‐imprinted polymer.© 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

The Discovery of Phenylbenzamide Derivatives as Grb7‐Based Antitumor Agents

Grb7 is a non‐catalytic protein, the overexpression of which has been associated with the proliferative and migratory potentials of cancer cells. Virtual screening strategies involving a shape‐based similarity search, molecular docking, and 2D‐similarity searches complemented by experimental binding studies (Thermofluor and isothermal titration calorimetry) resulted in the identification of nine novel phenylbenzamide‐based antagonists of the Grb7 SH2 domain. Moderate binding affinities were observed, ranging from K_d=32.3 μM for lead phenylbenzamide NSC 104999 ( 1 ) to K_d=1.1 μM for a structurally related compound, NSC 57148 ( 2 ). Deconvolution of the affinity data into its components revealed differences in lead binding, from being entropy based (lead 1 ) to enthalpically driven (NSC 100874 ( 3 ), NSC 55158 ( 4 ), and compound 2 ). Finally, the lead compound 1 was found to decrease the growth of MDA‐MB‐468 breast cancer cells, with an IC₅₀ value of 39.9 μM . It is expected that these structures will serve as novel leads in the development of Grb7‐based anticancer therapeutics.     

Probing Ligand Structure–Activity Relationships in Pregnane X Receptor (PXR): Efavirenz and 8‐Hydroxyefavirenz Exhibit Divergence in Activation

Efavirenz (EFV), an antiretroviral that interacts clinically with co‐administered drugs via activation of the pregnane X receptor (PXR), is extensively metabolized by the cytochromes P450. We tested whether its primary metabolite, 8‐hydroxyEFV (8‐OHEFV) can activate PXR and potentially contribute to PXR‐mediated drug–drug interactions attributed to EFV. Luciferase reporter assays revealed that despite only differing from EFV by an oxygen atom, 8‐OHEFV does not activate PXR. Corroborating this, treatment with EFV for 72 h elevated the mRNA abundance of the PXR target gene, Cyp3a11, by approximately 28‐fold in primary hepatocytes isolated from PXR‐humanized mice, whereas treatment with 8‐OHEFV did not result in a change in Cyp3A11 mRNA levels. FRET‐based competitive binding assays and isothermal calorimetry demonstrated that even with the lack of ability to activate PXR, 8‐OHEFV displays an affinity for PXR (IC₅₀ 12.1 μm ; K_D 7.9 μm ) nearly identical to that of EFV (IC₅₀ 18.7 μm ; K_D 12.5 μm ). The use of 16 EFV analogues suggest that other discreet changes to the EFV structure beyond the 8‐position are well tolerated. Molecular docking simulations implicate an 8‐OHEFV binding mode that may underlie its divergence in PXR activation from EFV.     

Binding properties of peptidic affinity ligands for plasmid DNA capture and detection

Peptides constructed from α‐helical subunits of the Lac repressor protein (LacI) were designed then tailored to achieve particular binding kinetics and dissociation constants for plasmid DNA purification and detection. Surface plasmon resonance was employed for quantification and characterization of the binding of double stranded Escherichia coli plasmid DNA (pUC19) via the lac operon (lacO) to “biomimics” of the DNA binding domain of LacI. Equilibrium dissociation constants (K_D), association (k_a), and dissociation rates (k_d) for the interaction between a suite of peptide sequences and pUC19 were determined. K_D values measured for the binding of pUC19 to the 47mer, 27mer, 16mer, and 14mer peptides were 8.8 ± 1.3 × 10^?10 M, 7.2 ± 0.6 × 10^?10 M, 4.5 ± 0.5 × 10^?8 M, and 6.2 ± 0.9 × 10^?6 M, respectively. These findings show that affinity peptides, composed of subunits from a naturally occurring operon–repressor interaction, can be designed to achieve binding characteristics suitable for affinity chromatography and biosensor devices. © 2008 American Institute of Chemical Engineers AIChE J, 2009     

Carbohydrate–PNA and Aptamer–PNA Conjugates for the Spatial Screening of Lectins and Lectin Assemblies

Nucleic acid architectures offer intriguing opportunities for the interrogation of structural properties of protein receptors. In this study, we performed a DNA‐programmed spatial screening to characterize two functionally distinct receptor systems: 1) structurally well‐defined Ricinus communis agglutinin (RCA₁₂₀), and 2) rather ill‐defined assemblies of L‐selectin on nanoparticles and leukocytes. A robust synthesis route that allowed the attachment both of carbohydrate ligands—such as N‐acetyllactosamine (LacNAc), sialyl‐Lewis‐X (sLe^X), and mannose—and of a DNA aptamer to PNAs was developed. A systematically assembled series of different PNA–DNA complexes served as multivalent scaffolds to control the spatial alignments of appended lectin ligands. The spatial screening of the binding sites of RCA₁₂₀ was in agreement with the crystal structure analysis. The study revealed that two appropriately presented LacNAc ligands suffice to provide unprecedented RCA₁₂₀ affinity (K_D=4 μM ). In addition, a potential secondary binding site was identified. Less dramatic binding enhancements were obtained when the more flexible L‐selectin assemblies were probed. This study involved the bivalent display both of the weak‐affinity sLe^X ligand and of a high‐affinity DNA aptamer. Bivalent presentation led to rather modest (sixfold or less) enhancements of binding when the self‐assemblies were targeted against L‐selectin on gold nanoparticles. Spatial screening of L‐selectin on the surfaces of leukocytes showed higher affinity enhancements (25‐fold). This and the distance–activity relationships indicated that leukocytes permit dense clustering of L‐selectin.