FimH antagonists: structure-activity and structure-property relationships for biphenyl α-D-mannopyranosides

Urinary tract infections (UTIs) are caused primarily by uropathogenic Escherichia coli (UPEC), which encode filamentous surface‐adhesive organelles called type 1 pili. FimH is located at the tips of these pili. The initial attachment of UPEC to host cells is mediated by the interaction of the carbohydrate recognition domain (CRD) of FimH with oligomannosides on urothelial cells. Blocking these lectins with carbohydrates or analogues thereof prevents bacterial adhesion to host cells and therefore offers a potential therapeutic approach for prevention and/or treatment of UTIs. Although numerous FimH antagonists have been developed so far, few of them meet the requirement for clinical application due to poor pharmacokinetics. Additionally, the binding mode of an antagonist to the CRD of FimH can switch from an in‐docking mode to an out‐docking mode, depending on the structure of the antagonist. In this communication, biphenyl α‐D ‐mannosides were modified to improve their binding affinity, to explore their binding mode, and to optimize their pharmacokinetic properties. The inhibitory potential of the FimH antagonists was measured in a cell‐free competitive binding assay, a cell‐based flow cytometry assay, and by isothermal titration calorimetry. Furthermore, pharmacokinetic properties such as log D, solubility, and membrane permeation were analyzed. As a result, a structure–activity and structure–property relationships were established for a series of biphenyl α‐D ‐mannosides.     

Kinetic Properties of Carbohydrate–Lectin Interactions: FimH Antagonists

The lectin FimH is terminally expressed on type 1 pili of uropathogenic Escherichia coli (UPEC), which is the main cause of urinary tract infections (UTIs). FimH enables bacterial adhesion to urothelial cells, the initial step of infection. Various mannose derivatives have been shown to antagonize FimH and are therefore considered to be promising therapeutic agents for the treatment of UTIs. As part of the preclinical development process, when the kinetic properties of FimH antagonists were examined by surface plasmon resonance, extremely low dissociation rates (k_off) were found, which is uncommon for carbohydrate–lectin interactions. As a consequence, the corresponding half‐lives (t_1/2) of the FimH antagonist complexes are above 3.6 h. For a therapeutic application, extended t_1/2 values are a prerequisite for success, since the target occupancy time directly influences the in vivo drug efficacy. The long t_1/2 value of the tested FimH antagonists further confirms their drug‐like properties and their high therapeutic potential.     

Antivirulence Isoquinolone Mannosides: Optimization of the Biaryl Aglycone for FimH Lectin Binding Affinity and Efficacy in the Treatment of Chronic UTI

Uropathogenic E. coli (UPEC) employ the mannose‐binding adhesin FimH to colonize the bladder epithelium during urinary tract infection (UTI). Previously reported FimH antagonists exhibit good potency and efficacy, but low bioavailability and a short half‐life in vivo. In a rational design strategy, we obtained an X‐ray structure of lead mannosides and then designed mannosides with improved drug‐like properties. We show that cyclizing the carboxamide onto the biphenyl B‐ring aglycone of biphenyl mannosides into a fused heterocyclic ring, generates new biaryl mannosides such as isoquinolone 22 (2‐methyl‐4‐(1‐oxo‐1,2‐dihydroisoquinolin‐7‐yl)phenyl α‐d ‐mannopyranoside) with enhanced potency and in vivo efficacy resulting from increased oral bioavailability. N‐Substitution of the isoquinolone aglycone with various functionalities produced a new potent subseries of FimH antagonists. All analogues of the subseries have higher FimH binding affinity than unsubstituted lead 22 , as determined by thermal shift differential scanning fluorimetry assay. Mannosides with pyridyl substitution on the isoquinolone group inhibit bacteria‐mediated hemagglutination and prevent biofilm formation by UPEC with single‐digit nanomolar potency, which is unprecedented for any FimH antagonists or any other antivirulence compounds reported to date.     

Improvement of Aglycone π-Stacking Yields Nanomolar to Sub-nanomolar FimH Antagonists

Antimicrobial resistance has become a serious concern for the treatment of urinary tract infections. In this context, an anti-adhesive approach targeting FimH, a bacterial lectin enabling the attachment of E. coli to host cells, has attracted considerable interest. FimH can adopt a low/medium-affinity state in the absence and a high-affinity state in the presence of shear forces. Until recently, mostly the high-affinity state has been investigated, despite the fact that a therapeutic antagonist should bind predominantly to the low-affinity state. In this communication, we demonstrate that fluorination of biphenyl α-d -mannosides leads to compounds with perfect π–π stacking interactions with the tyrosine gate of FimH, yielding low nanomolar to sub-nanomolar K_D values for the low- and high-affinity states, respectively. The face-to-face alignment of the perfluorinated biphenyl group of FimH ligands and Tyr48 was confirmed by crystal structures as well as ¹H,¹⁵N-HSQC NMR analysis. Finally, fluorination improves pharmacokinetic parameters predictive for oral availability.     

The Antiadhesive Strategy in Crohn′s Disease: Orally Active Mannosides to Decolonize Pathogenic Escherichia coli from the Gut

Blocking the adherence of bacteria to cells is an attractive complementary approach to current antibiotic treatments, which are faced with increasing resistance. This strategy has been particularly studied in the context of urinary tract infections (UTIs), in which the adhesion of pathogenic Escherichia coli strains to uroepithelial cells is prevented by blocking the FimH adhesin expressed at the tips of bacteria organelles called fimbriae. Recently, we extended the antiadhesive concept, showing that potent FimH antagonists can block the attachment of adherent‐invasive E. coli (AIEC) colonizing the intestinal mucosa of patients with Crohn′s disease (CD). In this work, we designed a small library of analogues of heptyl mannoside (HM), a previously identified nanomolar FimH inhibitor, but one that displays poor antiadhesive effects in vivo. The anomeric oxygen atom was replaced by a sulfur or a methylene group to prevent hydrolysis by intestinal glycosidases, and chemical groups were attached at the end of the alkyl tail. Importantly, a lead compound was shown to reduce AIEC levels in the feces and in the colonic and ileal mucosa after oral administration (10 mg kg^?1) in a transgenic mouse model of CD. The compound showed a low bioavailability, preferable in this instance, thus suggesting the possibility of setting up an innovative antiadhesive therapy, based on the water‐soluble and non‐cytotoxic FimH antagonists developed here, for the CD subpopulation in which AIEC plays a key role.     

Fragmenting the S100B–p53 Interaction: Combined Virtual/Biophysical Screening Approaches to Identify Ligands

S100B contributes to cell proliferation by binding the C terminus of p53 and inhibiting its tumor suppressor function. The use of multiple computational approaches to screen fragment libraries targeting the human S100B–p53 interaction site is reported. This in silico screening led to the identification of 280 novel prospective ligands. NMR spectroscopic experiments revealed specific binding at the p53 interaction site for a set of these compounds and confirmed their potential for further rational optimization. The X‐ray crystal structure determined for one of the binders revealed key intermolecular interactions, thus paving the way for structure‐based ligand optimization.     

Comparative study on structural features of α chitin from Xiphopenaeus kroyeri and its precipitated product from phosphoric acid solution

A sample of α chitin was obtained from shells of the shrimp Xiphopenaeus kroyeri by demineralization and deproteinization processes. This sample of native α chitin (NC) was dissolved in concentrated phosphoric acid and recovered by precipitation in an alkaline aqueous solution, giving rise to a sample named PC. Solid‐state carbon‐13 nuclear magnetic resonance (¹³C‐NMR), X‐ray diffraction, and atomic force microscopy (AFM) techniques were used to compare both samples and to investigate structural changes in α chitin under the action of phosphoric acid. ¹³C‐NMR experiments and X‐ray diffraction results revealed a high crystalline order in both samples. Structural differences were due to the higher distance between adjacent chains along the b axis and the consequent decrease in the number of intermolecular hydrogen bonds in the sample recovered from solution. While remarkable supramolecular differences could be observed in the fibrillar crystals of the NC sample, the PC sample was characterized by only one type of morphology. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 83: 151–159, 2002     

Synthesis and characterization of a novel oligosiloxane containing alternative ladderlike structure via charge‐transfer interaction

A novel oligosiloxane containing alternative ladderlike structure involving viologen groups has been prepared via donor–acceptor interaction‐assisted template polymerization. The monomer used as the electron‐donor component, N,N ′‐bis(3‐methyldimethoxyl‐silylpropyl)‐4,4′‐bipyridinium dihexafluorophosphate and its precursor, N,N ′‐bis(3‐methyldimethoxyl‐silylpropyl)‐4,4′‐bipyridinium dibromide were first synthesized successfully in high yield. This oligosiloxane, which displays interesting electrochromic properties, has been characterized by FTIR, UV–vis, ¹H NMR, ²⁹Si NMR, X‐ray diffraction (XRD), and vapour pressure osmometry (VPO). © 2001 Society of Chemical Industry     

NMR‐Guided Molecular Docking of a Protein–Peptide Complex Based on Ant Colony Optimization

Standard docking approaches used for the prediction of protein–ligand complexes in the drug development process have problems identifying the correct binding mode of large flexible ligands. Herein we show how additional experimental data from NMR experiments can be used to predict the binding mode of a mucin 1 (MUC‐1) pentapeptide recognized by the breast‐cancer‐selective monoclonal antibody SM3. Distance constraints derived from trNOE and saturation transfer difference NMR experiments are combined with the docking approach PLANTS. The resulting complex structures show excellent agreement with the NMR data and with a published X‐ray crystal structure. The method was then further tested on two complexes in order to demonstrate its more general applicability: T‐antigen disaccharide bound to Maclura pomifera agglutinin, and the inhibitor SBi279 bound to S100B protein. Our new approach has the advantages of being fully automatic, rapid, and unbiased; moreover, it is based on relatively easily obtainable experimental data and can greatly increase the reliability of the generated structures.     

The Discovery and Development of the N‐Substituted trans‐3,4‐Dimethyl‐4‐(3′‐hydroxyphenyl)piperidine Class of Pure Opioid Receptor Antagonists

N‐Substituted trans‐3,4‐dimethyl‐4‐(3‐hydroxyphenyl)piperidines are a class of pure opioid receptor antagonists with a novel pharmacophore. This opioid receptor antagonist pharmacophore was used as a lead structure to design and develop several interesting and useful opioid receptor antagonists. In this review we describe: 1) early SAR studies that led to the discovery of LY255582 and analogues that are nonselective opioid receptor antagonists developed for the treatment of obesity; 2) the discovery and commercialization of LY246736 (alvimopan; ENTEREG®), a peripherally selective opioid receptor antagonist that accelerates the time to upper and lower GI recovery following surgeries that include partial bowel resection with primary anastomosis; and 3) the discovery and development of the potent and selective κ opioid receptor antagonist JDTic and analogues as potential pharmacotherapies for treating depression, anxiety, and substance abuse (nicotine, alcohol, and cocaine). In addition, the use of JDTic for obtaining the X‐ray structure of the human κ opioid receptor is discussed.     

The High‐Pressure Characterization of Energetic Materials: 1‐Methyl‐5‐Nitramino‐1H‐Tetrazole

Pressure–volume relations and optical Raman and Infrared spectra of polycrystalline 1MNT have been obtained under quasi‐hydrostatic conditions up to 16 and 40 GPa, respectively, by using diamond anvil cell, synchrotron‐based angle‐resolved X‐ray diffraction, and microspectroscopy. The X‐ray measurements show that the pressure–volume relations remain smooth up to 16 GPa at room temperature, while vibrational measurements show no evidence of a phase transition to near 40 GPa. Anomalous increases of several vibrational intensities and bandwidths suggest that subtle molecular distortions and structural modifications occur in the crystal as pressure increases. Decompression experiments indicate the structural modifications are reversible.     

Synthesis and characterization of novel polyurethanes based on N1,N4‐bis[(4‐hydroxyphenyl)methylene]succinohydrazide hard segment

This article deals with the synthesis and characterization of novel polyurethanes (PUs) by the reaction between two aromatic diisocyanates (4,4′‐diphenylmethane diisocyanate and tolylene 2,4‐diisocyanate) and two aliphatic diisocyanates (isophorone diisocyanate and hexamethylene diisocyanate) with N¹,N⁴‐bis[(4‐hydroxyphenyl)methylene]succinohydrazide, which acted as hard segment. UV–vis, FTIR, ¹H NMR, ¹³C NMR, and DSC/TGA analytical technique has been used to determine the structural characterization and thermal properties of the hard segmented PUs. X‐ray diffraction revealed that PUs contained semicrystalline and amorphous regions that varied depending upon the nature of the backbone structures. PUs were soluble in polar aprotic solvents. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Galectin‐3‐Binding Glycomimetics that Strongly Reduce Bleomycin‐Induced Lung Fibrosis and Modulate Intracellular Glycan Recognition

Discovery of glycan‐competitive galectin‐3‐binding compounds that attenuate lung fibrosis in a murine model and that block intracellular galectin‐3 accumulation at damaged vesicles, hence revealing galectin‐3–glycan interactions involved in fibrosis progression and in intracellular galectin‐3 activities, is reported. 3,3′‐Bis‐(4‐aryltriazol‐1‐yl)thiodigalactosides were synthesized and evaluated as antagonists of galectin‐1, ‐2, ‐3, and ‐4 N‐terminal, ‐4 C‐terminal, ‐7 and ‐8 N‐terminal, ‐9 N‐terminal, and ‐9 C‐terminal domains. Compounds displaying low‐nanomolar affinities for galectins‐1 and ‐3 were identified in a competitive fluorescence anisotropy assay. X‐ray structural analysis of selected compounds in complex with galectin‐3, together with galectin‐3 mutant binding experiments, revealed that both the aryltriazolyl moieties and fluoro substituents on the compounds are involved in key interactions responsible for exceptional affinities towards galectin‐3. The most potent galectin‐3 antagonist was demonstrated to act in an assay monitoring galectin‐3 accumulation upon amitriptyline‐induced vesicle damage, visualizing a biochemically/medically relevant intracellular lectin–carbohydrate binding event and that it can be blocked by a small molecule. The same antagonist administered intratracheally attenuated bleomycin‐induced pulmonary fibrosis in a mouse model with a dose/response profile comparing favorably with that of oral administration of the marketed antifibrotic compound pirfenidone.     

Synthesis and Characteristics of Dodecyl Isopropylolamine and Derived Surfactants

Dodecyl isopropylolamine has been synthesized on the basis of dodecylamine and propylene oxide. The structure of dodecyl isopropanolamine has been determined by X‐ray diffraction, elemental analysis, IR‐ and NMR‐spectroscopic methods. Ionic surfactants have been synthesized by interaction of dodecyl isopropylolamine with various acids (HCl, HBr, acetic and propionic) and alkyl halides (methyl iodide, ethyl bromide and n‐propyl bromide). Colloidal‐chemical parameters, petroleum‐collecting and petroleum dispersing capacities of the synthesized cationic surfactants have been studied.     

Self‐assembled centimetre‐sized rods obtained in the oxidation of o‐phenylenediamine and aniline

Morphologically well‐defined rods of approximately 1 cm in length are effectively and economically obtained by mixing ortho‐phenylenediamine (30 mmol L^?1) with ammonium persulfate (12.5 mmol L^?1) in an acidic solution (0.37 mol L^?1 HCl) at room temperature with and without the presence of 50 mmol L^?1 aniline. These self‐assembled, morphologically uniform products can be potentially scaled up and used as morphological templates to fabricate well‐defined structures of other materials such as conducting polymers. The products were characterized using Raman, UV‐visible, high‐resolution NMR (¹H and ¹³C) and mass spectroscopies, X‐ray diffraction, scanning electron microscopy and elemental analysis. Apart from certain differences in visual appearance and in X‐ray diffractograms, other analytical data suggest that there are no structural changes upon addition of aniline into the reaction mixture. NMR and mass spectra imply that all syntheses carried out either with or without aniline result in a mixture of two products, attributed to 2,3‐phenazinediamine and 3‐aminophenazin‐2‐ol. A formation mechanism based on hydrogen bonding and π–π stacking has been proposed. © 2015 Society of Chemical Industry     

Fibrous long‐chain organic acid cellulose esters and their characterization by diffuse reflectance FTIR spectroscopy,solid‐state CP/MAS 13C‐NMR,and X‐ray diffraction

Unsaturated and saturated organic acids with 11 and 18 carbon atoms, respectively, were used in a heterogeneous esterification reaction in the pyridine/toluene sulfonyl chloride system to prepare fibrous cellulose esters with different degrees of substitution. Highly bleached sulfite cellulose fibers were esterified during a 1‐ or 2‐h reaction time with the following organic acids: undecylenic acid, undecanoic acid, oleic acid, and stearic acid. In all cases, the heterogeneous esterification yielded partially substituted cellulose esters retaining their fibrous structure. The substitution reaction was confirmed by diffuse reflectance infrared spectroscopy and the chemical structures of cellulose esters were identified by solid‐state CP/MAS ¹³C‐NMR (75.3 MHz). X‐ray diffraction analyses showed broadening of the diffraction peaks with a higher degree of substitution of cellulose esters, which suggests structural changes within the cellulose fibers. Because the broadening peaks of X‐ray spectra or the unassigned C‐4 region of substituted cellulose chains in NMR spectra do not allow the calculation of dimensional changes of cellulose crystallites in cellulose esters, the lateral dimensions of crystallites in only cellulose fibers were calculated. The value derived from NMR (4.6 nm) differs by about 11% when compared with the value calculated from X‐ray diffraction data (4.1 nm). © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 1354–1365, 2000     

Poplar wood–methylol urea composites prepared by in situ polymerization. II. Characterization of the mechanism of wood modification by methylol urea

A prepolymer was used to prepare wood/prepolymer composites by a pulse‐dipping machine. The mechanical properties and dimensional stability were evaluated. The characterization of natural and modified woods was performed by Fourier transform infrared spectroscopy, ¹³C‐NMR spectroscopy, X‐ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) with energy‐dispersive X‐ray analysis (EDXA). Cross‐polarization/magic‐angle spinning ¹³C‐NMR analysis revealed that the in situ polymerization between the prepolymer and the hydroxyls in the wood structure took place with the reduction of hydroxyl groups. XPS analysis indicated that the content of carbon decreased, whereas the content of oxygen increased. SEM–EDXA indicated a good dispersion of the modifier in the wood fiber and other vertical cells. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 42406.     

Synthesis and characterization of hybrid clay/poly (N,N‐dimethylaminoethyl methacrylate) nanocomposites

Four quaternary ammonium salt monomers (2a–d) were synthesized from N,N‐dimethylaminoethyl methacrylate and subsequently polymerized to afford cationic polymers (3a–d). The synthesized monomers and polymers were characterized by Fourier transform infrared (FTIR) and proton nuclear magnetic resonance (¹H NMR) spectroscopy. Molecular weights of the synthesized polymers were determined using gel permeation chromatography. Polymer/clay nanocomposites (4a–d) were prepared using solution‐intercalation method and characterized by FTIR, X‐ray diffraction, high‐resolution transmission electron microscopy, energy dispersive X‐ray, and thermogravimetric analysis. Data analysis showed that polymer/clay nanocomposites have intercalated structure. The dielectric properties of the polymer/clay nanocomposites were studied as a function of both temperature and frequency. POLYM. COMPOS., 37:2950–2959, 2016. © 2015 Society of Plastics Engineers     

The High‐Pressure Characterization of Energetic Materials: Diaminotetrazolium Nitrate (HDAT‐NO3)

In‐situ high‐pressure room temperature synchrotron X‐ray diffraction and optical Raman and infrared spectroscopy were used to examine the structural properties, equation of state, and vibrational dynamics of diaminotetrazolium nitrate (HDAT‐NO₃). The X‐ray measurements show that the pressure–volume relations remain smooth to 12 GPa. X‐ray diffraction measurements at pressures above 12 GPa were not possible in this study because of sample decomposition resulting from several factors. X‐ray diffraction reveals no indication of a phase transition to at least 12 GPa, but slight variations in the c/b unit cell ratio suggests modifications within the hydrogen bonding sub‐lattice. Vibrational measurements show the ambient phase of HDAT‐NO₃ to remain the dominant phase to 33 GPa.     

C3 Halogen and C8′′ Substituents on Stilbene Arotinoids Modulate Retinoic Acid Receptor Subtype Function

The synthesis and biological evaluation of the entire series of C3‐halogenated derivatives and bulkier substituents at the C8′′ position of the parent stilbene‐based RARβ‐selective agonist BMS641 4 c was undertaken. The synthesis uses an E‐selective Horner–Wadsworth–Emmons (HWE) condensation of C8‐substituted C5‐dimethyl dihydronaphthaldehyde and the benzylic phosphonates derived from the C3‐halogenated benzoates to construct the stilbene skeleton. Transactivation studies revealed the synergistic effect of small halogen atoms at C3 (F, Cl) and the moderately bulky phenyl group at C8′′ (in 4 b and 4 c ) to achieve RARβ selectivity. Our results, supported by computational studies, provide a structural rationale for the mixed agonist–antagonist activities of these arotinoids, which are potent agonists of the RARβ subtype and antagonists of the RARα paralogue. Moreover, transitions from partial agonists to inverse agonists and antagonists can be accomplished with the incorporation of the same halogen atoms into the structures of known modulators BMS701 ( 5 a ) and BMS493 ( 6 a ), which have bulkier substituents than phenyl (p‐tolyl and phenylethynyl, respectively) at C8′′. Conversely, incorporation of halogen atoms in 6 a converted the ligand from an RARβ inverse agonist ( 6 b ) to an antagonist ( 6 c ) or an agonist ( 6 d ). Amazingly, 6 a – c commonly acted as inverse agonists for RARα, while 6 d and 6 e acted as regular RARα antagonists, not affecting co‐repressor interaction. In the case of the mixed agonist/antagonist 5 a , C3‐halogenation yields inverse RARα and RARβ agonists ( 5 b – d ) with the exception of iodinated 5 e , which is a regular antagonist for both these receptors. Because RARβ gene expression is frequently deleted or epigenetically silenced in several tumor cells, the novel repertoire of receptor and function‐selective RAR agonists, mixed agonist/antagonists, regular antagonists, and inverse agonists will be useful in the elucidation of the mechanism of tumor suppression by retinoids.