Development of Pseudomonas aeruginosa Lectin LecA Inhibitor by using Bivalent Galactosides Supported on Polyproline Peptide Scaffolds

LecA is a galactose‐binding tetrameric lectin from Pseudomonas aeruginosa involved in infection and biofilm formation. The emergent antibiotic resistance of P. aeruginosa has made LecA a promising pharmaceutical target to treat such infections. To develop LecA inhibitors, we exploit the unique helical structure of polyproline peptides to create a scaffold that controls the galactoside positions to fit their binding sites on LecA. With a modular scaffold design, both the galactoside ligands and the inter‐ligand distance can be altered conveniently. We prepared scaffolds with spacings of 9, 18, 27, and 36 Å for ligand conjugation and found that glycopeptides with galactosides ligands three helical turns (27 Å) apart best fit LecA. In addition, we tested different galactose derivatives on the selected scaffold (27 Å) to improve the binding avidity to LecA. The results validate a new multivalent scaffold design and provide useful information for LecA inhibitor development.     

Toward the Rational Design of Galactosylated Glycoclusters That Target Pseudomonas aeruginosa Lectin A (LecA): Influence of Linker Arms That Lead to Low‐Nanomolar Multivalent Ligands

Anti‐infectious strategies against pathogen infections can be achieved through antiadhesive strategies by using multivalent ligands of bacterial virulence factors. LecA and LecB are lectins of Pseudomonas aeruginosa implicated in biofilm formation. A series of 27 LecA‐targeting glycoclusters have been synthesized. Nine aromatic galactose aglycons were investigated with three different linker arms that connect the central mannopyranoside core. A low‐nanomolar (K_d=19 nm , microarray) ligand with a tyrosine‐based linker arm could be identified in a structure–activity relationship study. Molecular modeling of the glycoclusters bound to the lectin tetramer was also used to rationalize the binding properties observed.     

Tetravalent Pseudomonas aeruginosa Adhesion Lectin LecA Inhibitor for Enhanced Biofilm Inhibition

A potent divalent ligand of the Pseudomonas aeruginosa adhesion lectin LecA was elaborated into a tetravalent version. A polyethylene glycol (PEG) spacer was introduced to link two divalent galactosides. Each of the two divalent ligands contained a rigid spacer with a central phenyl group that is bridged by the PEG moiety. The resulting tetravalent ligand was found to bind LecA in the nanomolar range involving all of its sugar (sub)ligands. Analytical ultracentrifugation studies clearly showed that the tetravalent ligand was capable of aggregation the LecA tetramers in contrast to the divalent ligands. The aggregator behavior was found to be of importance in P. aeruginosa biofilm formation inhibition. Despite the weaker affinity it was a considerably better biofilm inhibitor with half inhibitory values around the 28 micromolar range.     

Neutralizing the Impact of the Virulence Factor LecA from Pseudomonas aeruginosa on Human Cells with New Glycomimetic Inhibitors

Bacterial adhesion, biofilm formation and host cell invasion of the ESKAPE pathogen Pseudomonas aeruginosa require the tetravalent lectins LecA and LecB, which are therefore drug targets to fight these infections. Recently, we have reported highly potent divalent galactosides as specific LecA inhibitors. However, they suffered from very low solubility and an intrinsic chemical instability due to two acylhydrazone motifs, which precluded further biological evaluation. Here, we isosterically substituted the acylhydrazones and systematically varied linker identity and length between the two galactosides necessary for LecA binding. The optimized divalent LecA ligands showed improved stability and were up to 1000-fold more soluble. Importantly, these properties now enabled their biological characterization. The lead compound L2 potently inhibited LecA binding to lung epithelial cells, restored wound closure in a scratch assay and reduced the invasiveness of P. aeruginosa into host cells.     

Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging

Biofilm formation by pathogenic bacteria is a hallmark of chronic infections. In many cases, lectins play key roles in establishing biofilms. The pathogen Pseudomonas aeruginosa often exhibiting various drug resistances employs its lectins LecA and LecB as virulence factors and biofilm building blocks. Therefore, inhibition of the function of these proteins is thought to have potential in developing “pathoblockers” preventing biofilm formation and virulence. A covalent lectin inhibitor specific to a carbohydrate binding site is described for the first time. Its application in the LecA‐specific in vitro imaging of biofilms formed by P. aeruginosa is also reported.     

AFM investigation of Pseudomonas aeruginosa lectin LecA (PA-IL) filaments induced by multivalent glycoclusters

Atomic force microscopy reveals that Pseudomonas aeruginosa LecA (PA-IL) and a tetra-galactosylated 1,3-alternate calix[4]arene-based glycocluster self-assemble according to an aggregative chelate binding mode to create monodimensional filaments. Lectin oligomers are identified along the filaments and defects in chelate binding generate branches and bifurcations. A molecular model with alternate 90° orientation of LecA tetramers is proposed to describe the organisation of lectins and glycoclusters in the filaments.     

Stereoselective Synthesis of Fluorinated Galactopyranosides as Potential Molecular Probes for Galactophilic Proteins: Assessment of Monofluorogalactoside–LecA Interactions

The replacement of hydroxyl groups by fluorine atoms on hexopyranoside scaffolds may allow access to invaluable tools for studying various biochemical processes. As part of ongoing activities toward the preparation of fluorinated carbohydrates, a systematic investigation involving the synthesis and biological evaluation of a series of mono- and polyfluorinated galactopyranosides is described. Various monofluorogalactopyranosides, a trifluorinated, and a tetrafluorinated galactopyranoside have been prepared using a Chiron approach. Given the scarcity of these compounds in the literature, in addition to their synthesis, their biological profiles were evaluated. Firstly, the fluorinated compounds were investigated as antiproliferative agents using normal human and mouse cells in comparison with cancerous cells. Most of the fluorinated compounds showed no antiproliferative activity. Secondly, these carbohydrate probes were used as potential inhibitors of galactophilic lectins. The first transverse relaxation-optimized spectroscopy (TROSY) NMR experiments were performed on these interactions, examining chemical shift perturbations of the backbone resonances of LecA, a virulence factor from Pseudomonas aeruginosa. Moreover, taking advantage of the fluorine atom, the ¹⁹F NMR resonances of the monofluorogalactopyranosides were directly monitored in the presence and absence of LecA to assess ligand binding. Lastly, these results were corroborated with the binding potencies of the monofluorinated galactopyranoside derivatives by isothermal titration calorimetry experiments. Analogues with fluorine atoms at C-3 and C-4 showed weaker affinities with LecA as compared to those with the fluorine atom at C-2 or C-6. This research has focused on the chemical synthesis of “drug-like” low-molecular-weight inhibitors that circumvent drawbacks typically associated with natural oligosaccharides.     

Functionalization of a Rigid Divalent Ligand for LecA,a Bacterial Adhesion Lectin

The bacterial adhesion lectin LecA is an attractive target for interference with the infectivity of its producer P. aeruginosa. Divalent ligands with two terminal galactoside moieties connected by an alternating glucose-triazole spacer were previously shown to be very potent inhibitors. In this study, we chose to prepare a series of derivatives with various new substituents in the spacer in hopes of further enhancing the LecA inhibitory potency of the molecules. Based on the binding mode, modifications were made to the spacer to enable additional spacer–protein interactions. The introduction of positively charged, negatively charged, and also lipophilic functional groups was successful. The compounds were good LecA ligands, but no improved binding was seen, even though altered thermodynamic parameters were observed by isothermal titration calorimetry (ITC).     

Structure‐Based Optimization of the Terminal Tripeptide in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting LecA

The galactopeptide dendrimer GalAG2 ((β‐Gal‐OC₆H₄CO‐Lys‐Pro‐Leu)₄(Lys‐Phe‐Lys‐Ile)₂Lys‐His‐Ile‐NH₂) binds strongly to the Pseudomonas aeruginosa (PA) lectin LecA, and it inhibits PA biofilms, as well as disperses already established ones. By starting with the crystal structure of the terminal tripeptide moiety GalA‐KPL in complex with LecA, a computational mutagenesis study was carried out on the galactotripeptide to optimize the peptide–lectin interactions. 25 mutants were experimentally evaluated by a hemagglutination inhibition assay, 17 by isothermal titration calorimetry, and 3 by X‐ray crystallography. Two of these tripeptides, GalA‐KPY (dissociation constant (K_D)=2.7 μM ) and GalA‐KRL (K_D=2.7 μM ), are among the most potent monovalent LecA ligands reported to date. Dendrimers based on these tripeptide ligands showed improved PA biofilm inhibition and dispersal compared to those of GalAG2 , particularly G2KPY ((β‐Gal‐OC₆H₄CO‐Lys‐Pro‐Tyr)₄(Lys‐Phe‐Lys‐Ile)₂Lys‐His‐Ile‐NH₂). The possibility to retain and even improve the biofilm inhibition in several analogues of GalAG2 suggests that it should be possible to fine‐tune this dendrimer towards therapeutic use by adjusting the pharmacokinetic parameters in addition to the biofilm inhibition through amino acid substitutions.     

Inhibition of Ligand Binding Ability of Three Porphyrins by an Organic Effector

A stimulus‐responsive receptor 1 was designed and prepared to control the ligand‐binding ability of three active sites, two zinc tetraphenylporphyrin units (P1) and one zinc diethynyldiphenylporphyrin unit (P2), with one effector molecule 2 . Bulky hexarylbenzene units were incorporated as shielding panels in the middle of the flexible side arms of 1 . Spectroscopic titrations indicated that a stable supramolecular complex 1 ? 2 (K _{1 ? 2} =6.7×10⁶ m ^?1) was produced by the cooperative formation of multiple hydrogen and coordination bonds. As a result, the binding of a ligand to P1 was inhibited by 2 in a competitive manner. Additionally, the formation of 1 ? 2 brought about conformational restriction of the side arms to cover both faces of P2 with the shielding panels. The binding constant of 4‐phenylpyridine with P2 in 1 ? 2 decreased to 8.9 % of that in 1 . Namely, the ligand‐binding ability of P2 was inhibited according to an allosteric mechanism.     

Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures

Hydration is a critical factor in the ligand binding process. Herein, to examine the hydration states of ligand binding sites, the three-dimensional distribution function for the water oxygen site, g_O( r ) , is computed for 3,706 ligand-free protein structures based on the corresponding small molecule–protein complexes using the 3D-RISM theory. For crystallographic waters (CWs) close to the ligand, g_O( r ) reveals that several CWs are stabilized by interaction networks formed between the ligand, CW, and protein. Based on the g_O( r ) for the crystallographic binding pose of the ligand, hydrogen bond interactions are dominant in the highly hydrated regions while weak interactions such as CH-O are dominant in the moderately hydrated regions. The polar heteroatoms of the ligand occupy the highly hydrated and moderately hydrated regions in the crystallographic (correct) and wrongly docked (incorrect) poses, respectively. Thus, the g_O( r ) of polar heteroatoms may be used to distinguish the correct binding poses.     

Synthesis,physicochemical characterization,geometric structure and molecular docking of new biologically active ferrocene based Schiff base ligand with transition metal ions

Physicochemical studies were performed to study new ferrocene based Schiff base ligand (HL), (Z)‐(4‐(1‐((2‐carboxycyclohexa‐2,4‐dien‐1‐yl)imino)ethyl)[bis(η ⁵ cyclopenta‐1,3‐dien‐1 yl)]iron with some transition metal ions to form a series of ferrocenyl derivatives bearing transition metal complexes of the type [M(L)Cl(H₂O)₃] (M = Ni(II), Cu(II)), [M(L)Cl(H₂O)₃]nH₂O (M = Mn(II) (n = 1), Co(II) (n = 1), Zn(II) (n = 2) and Cd(II) (n = 3)) and [M(L)Cl(H₂O)₃]Cl.nH₂O (M = Cr(III) (n = 2) and Fe(III) (n = 1)). The new ligand and metal ion complexes have been prepared and characterized by IR, UV‐Vis, ¹H‐NMR, TG/DTA, elemental analysis and mass spectrometry. The TGA/DTG analysis revealed that the ferrocene precursors decompose spontaneously to form iron(II) oxide. The molecular and electronic structure of the ligand (HL) was optimized theoretically and the quantum chemical parameters were calculated. The molecular structure with a variety of functionalities can be used to investigate the coordination sites and the total charge density around each atom. DFT‐based molecular orbital energy calculations of the new ligand have been also studied. All of the complexes were screened against a panel of Gram (+) bacteria: Streptococcus pneumoniae and Bacillis subtilis , Gram (−) bacteria: Pseudomonas aeruginosa and Escherichia coli and panel of fungi: Aspergillus fumigatu , Syncephalastrum racemosum , Geotricum candidum and Candida albicans . Anticancer activity screening for the tested compounds using 4 different concentrations of HL ligand against human tumor cells of breast cancer cell line MCF‐7 were obtained. Molecular docking was used to predict the binding between HL ligand and human‐DNA‐Topo I complex (PDB ID: 1SC7), the receptors of breast cancer mutant oxidoreductase (PDB ID: 3HB5), crystal structure of Escherichia coli (PDB ID: 3T88), to identify the binding mode and the crucial functional groups interacting with the three proteins.     

Two Distinct Thermal Stabilities of DNA and Enzymatic Activities of DNase I in a Multistep Assembly with Carbazole Ligands: Different Binding Characteristics for Duplex and Quadruplex DNA

A partially hydrophobic carbazole ligand ((Im⁺)₂Cz: 2,2′‐(9‐ethyl‐9 H‐carbazole‐3,6‐diyl)bis(ethyne‐2,1‐diyl)bis(1,3‐dimethyl‐1 H‐imidazol‐3‐ium)) adopts two different binding states (binding states I and II) in its interactions with calf‐thymus (ct‐) DNA. Two distinct binding states were identified by biphasic UV/Vis and circular dichroism (CD) spectral changes during the titration of DNA into the carbazole ligand. At low concentrations of ct‐DNA, (Im⁺)₂Cz binds to nearly every part of ct‐DNA (binding state I). By contrast, an increased concentration of ct‐DNA results in a switch in the DNA‐binding state, so that the ligands are bound per five DNA base pairs. Similarly, a monocationic carbazole ligand (Im⁺Cz: 2‐((6‐bromo‐9‐ethyl‐9 H‐carbazol‐3‐yl)ethynyl)‐1,3‐dimethyl‐1 H‐imidazol‐3‐ium) also shows biphasic UV/Vis spectral changes during the titration of ct‐DNA into Im⁺Cz, which suggests two different binding states of the Im⁺Cz ligand with ct‐DNA. The stepwise equilibrium of the ligand–DNA‐complex formation is capable of switching the thermal stability of ct‐DNA, as well as the enzymatic activity of deoxyribonuclease (DNase I). In binding state I, the (Im⁺)₂Cz ligands interact with nearly every base pair in ct‐DNA and stabilize the double‐helix structure, which results in a larger increase in the melting temperature of the ct‐DNA than that observed with binding state II. On the other hand, the (Im⁺)₂Cz ligand significantly reduces the enzymatic activity of DNase I in binding state I, although the enzymatic activity is recovered once the binding state of the ligand–DNA complex is changed to binding state II. The (Im⁺)₂Cz ligand was also employed as a binder for G‐quadruplex DNA. In contrast to the stepwise complex formation between (Im⁺)₂Cz and ct‐DNA, (Im⁺)₂Cz shows a monotonous UV/Vis spectral response during the titration of G‐quadruplex DNA into (Im⁺)₂Cz, which suggests a single binding state for (Im⁺)₂Cz with G‐quadruplex DNA.     

Determining PPARγ-ligand binding affinity using fluorescent assay with cis -parinaric acid as a probe

Upon the study of small-molecules binding to proteins, the traditional methods for calculating dissociation constants (K _d and K _i ) have shortcomings in dealing with the single binding site models. In this paper, two equations have been derived to solve this problem. These two equations are independent of the total concentration or initial degree of saturation of receptor and the activity of the competitive molecule. Through nonlinear fitting against these two equations, K _d value of a probe can be obtained by binding assay, and K _i value of a ligand can be obtained by competitive assay. Moreover, only the total concentrations of receptor([R]_t), ligand([L]_t) and probe([P]_t) are required for the data fitting. In this work, K _i values of some typical ligands of PPARγ were successfully determined by use of our equations, among which the K _i value of PPARγ-LY171883 was reported for the first time.     

Determination of the binding epitope of lidocaine with AGP: minimizing the effects of nonspecific binding in saturation transfer difference experiments

The ligand epitope map and the effect of nonspecific binding is assessed for lidocaine binding to α₁-acid glycoprotein using the saturation transfer difference nuclear magnetic resonance experiment performed as a function of the ligand/protein ratio. The experimental design tested two different approaches for preparing solutions with various ligand/protein ratios; holding the protein concentration constant and increasing the ligand concentration; and holding the ligand concentration constant while decreasing the protein concentration. Nonspecific binding effects were more prevalent in experiments in which the ligand concentration was increased, although spectra with higher signal-to-noise ratios were obtained under these conditions. The epitope map determined for achiral lidocaine is compared with previously determined results for the (R)- and (S)-enantiomers of propranolol. The weaker binding affinity of lidocaine may be partially attributed to steric hindrance by the lidocaine N-ethyl groups which may prevent close contact of the lidocaine amine with the negatively charged amino acids at the apex of the protein binding pocket.     

A phosphoranide (10-P-4) anion coordinating to transition metals,as a Lewis base and a π-acceptor

The reaction of 10-P-5 hydridophosphorane 6 with KH provides the 10-P-4 potassium phosphoranide anion 7a . Anion 7a reacts with CpFe(CO)₂I and BrAu(PEt₃) to replace the halide with the phosphoranide as a monodentate ligand forming 8 and 9 . The X-ray structure of 8 shows that the equatorial—Fe(CO)₂Cp ligand of 8 makes the apical P O bonds (1.824 Å) longer than the P O bonds (1.80 Å) of the phosphoranide oxide anion 10 . The P O bonds (1.75 Å) of 6 , with an equatorial proton ligand, are still shorter. This provides evidence that the—Fe(CO)₂Cp ligand is not only a sigma-acceptor Lewis acid ligand, but also a pi-donor that transfers electrons into the O P O three-center bond's anti-bonding orbital to increase its P—O bond lengths. It is a better pi-donor than the  O⁻ pi-donor of phosphoranide oxide 10 .     

Synthesis,characterization of Schiff base metal complexes and their biological investigation

A new Schiff base ligand named (E)‐2‐(((3‐aminophenyl)imino)methyl)phenol (HL) was prepared through condensation reaction of m‐phenylenediamine and 2‐hydroxybenzaldehyde in 1:1 molar ratio. The new ligand was characterized by elemental analysis and spectral techniques. The coordination behavior of a series of transition metal ions named Cr (III), Mn (II), Fe (III), Co (II), Ni (II), Cu (II), Zn (II) and Cd (II) with the newly prepared Schiff base ligand (HL) is reported. The nature of bonding and the stereochemistry of the complexes have been deduced from elemental analyses, IR, UV–Vis, ¹H NMR, mass, electronic spectra, magnetic susceptibility and conductivity measurements and further their thermal stability was confirmed by thermogravimetric analysis (TG). From IR spectra, it was observed that the ligand is a neutral tridentate ligand coordinates to the metal ions through protonated phenolic oxygen, azomethine nitrogen and nitrogen atom of NH₂ group. The existence, the number and the position of the water molecules was studied by thermal analysis. The molecular structures of the Schiff base ligand (HL) and its metal complexes were optimized theoretically and the quantum chemical parameters were calculated. The synthesized ligand and its complexes were screened for antimicrobial activities against bacterial species (Staphylococcus aureus and Bacillis subtilis, (gram positive bacteria)), (Salmonella SP., Escherichia coli and Pseudomonas aeruginosa, (gram negative bacteria)) and fungi (Aspergillus fumigatus and Candida albicans). The complexes were found to possess high biological activities against different organisms. Molecular docking was used to predict the efficiency of binding between Schiff base ligand (HL) and both receptors of Escherichia coli (3 T88) and Staphylococcus aureus (3Q8U). The receptor of Escherichia coli (3 T88) showed best interaction with Schiff base ligand (HL) compared to receptor of Staphylococcus aureu (3Q8U).     

Fine Tuning of Heme Reactivity: Hydrogen-Bonding and Dipole Interactions Affecting Ligand Binding to Hemoproteins

Heme reactivity in hemoproteins is governed by the microenvironment near the ligand binding site. In order to quantify polarity effects on heme ligand binding, the kinetics of O₂ and CO binding have been measured for a series of synthetic heme models equipped with a range of groups of varying dipole moments positioned near the heme coordination site. For hemes with polar aprotic groups, both O₂ on (k′) and off rates (k) are found to be dependent on the dipole moment. For model systems containing protic groups, the O₂ off rate is substantially reduced due to hydrogen bonding with the coordinated O₂. The hydrogen-bonding stabilization is estimated to be 0.7 and 1.6 kcal/mol for an alcohol and a secondary amide, respectively. CO binding displays little correlation with a polarity effect; instead it seems to depend upon the size and position of the polar group.     

Iron pyrrole‐based PNP pincer ligand complexes as catalyst precursors

The structure of a pincer ligand consists of a backbone and two `arms' which typically contain a P or N atom. They are tridentate ligands that coordinate to a metal center in a meridional configuration. A series of three iron complexes containing the pyrrole‐based PNP pincer ligand 2,5‐bis[(diisopropylphosphanyl)methyl]pyrrolide (PN^pyrP) has been synthesized. These complexes are possible precursors to new iron catalysts. {2,5‐Bis[(diisopropylphosphanyl)methyl]pyrrolido‐κ³P ,N ,P ′}carbonylchlorido(trimethylphosphane‐κP )iron(II), [Fe(C₁₈H₃₄NP₂)Cl(C₃H₉P)(CO)] or [Fe(PN^pyrP)Cl(PMe₃)(CO)], (I), has a slightly distorted octahedral geometry, with the Cl and CO ligands occupying the apical positions. {2,5‐Bis[(diisopropylphosphanyl)methyl]pyrrolido‐κ³P ,N ,P ′}chlorido(pyridine‐κN )iron(II), [Fe(C₁₈H₃₄NP₂)Cl(C₅H₅N)] or [Fe(PN^pyrP)Cl(py)] (py is pyridine), (II), is a five‐coordinate square‐pyramidal complex, with the pyridine ligand in the apical position. {2,5‐Bis[(diisopropylphosphanyl)methyl]pyrrolido‐κ³P ,N ,P ′}dicarbonylchloridoiron(II), [Fe(C₁₈H₃₄NP₂)Cl(CO)₂] or [Fe(PN^pyrP)Cl(CO)₂], (III), is structurally similar to (I), but with the PMe₃ ligand replaced by a second carbonyl ligand from the reaction of (II) with CO. The two carbonyl ligands are in a cis configuration, and there is positional disorder of the chloride and trans carbonyl ligands.     

Switching the Mechanism of NADH Photooxidation by Supramolecular Interactions

A series of three Ru(II) polypyridine complexes was investigated for the selective photocatalytic oxidation of NAD(P)H to NAD(P)⁺ in water. A combination of (time-resolved) spectroscopic studies and photocatalysis experiments revealed that ligand design can be used to control the mechanism of the photooxidation: For prototypical Ru(II) complexes a ¹O₂ pathway was found. Rudppz ([(tbbpy)₂Ru(dppz)]Cl₂, tbbpy=4,4'-di-tert-butyl-2,2'-bipyridine, dppz=dipyrido[3,2-a:2′,3′-c]phenazine), instead, initiated the cofactor oxidation by electron transfer from NAD(P)H enabled by supramolecular binding between substrate and catalyst. Expulsion of the photoproduct NAD(P)⁺ from the supramolecular binding site in Rudppz allowed very efficient turnover. Therefore, Rudppz permits repetitive selective assembly and oxidative conversion of reduced naturally occurring nicotinamides by recognizing the redox state of the cofactor under formation of H₂O₂ as additional product. This photocatalytic process can fuel discontinuous photobiocatalysis.