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1.
Carbohydrate-binding proteins (lectins) are auspicious targets in drug discovery to combat antimicrobial resistance; however, their non-carbohydrate drug-like inhibitors are still unavailable. Here, we present a druggable pocket in a β-propeller lectin BambL from Burkholderia ambifaria as a potential target for allosteric inhibitors. This site was identified employing 19F NMR fragment screening and a computational pocket prediction algorithm SiteMap. The structure–activity relationship study revealed the most promising fragment with a dissociation constant of 0.3±0.1 mM and a ligand efficiency of 0.3 kcal mol?1 HA?1 that affected the orthosteric site. This effect was substantiated by site-directed mutagenesis in the orthosteric and secondary pockets. Future drug-discovery campaigns that aim to develop small molecule inhibitors can benefit from allosteric sites in lectins as a new therapeutic approach against antibiotic-resistant pathogens.  相似文献   

2.
Heat Shock Protein 70s (HSP70s) are key molecular chaperones that are overexpressed in many cancers and often associated with metastasis and poor prognosis. It has proven difficult to develop ATP-competitive, drug-like small molecule inhibitors of HSP70s due to the flexible and hydrophilic nature of the HSP70 ATP-binding site and its high affinity for endogenous nucleotides. The aim of this study was to explore the potential for the inhibition of HSP70 through alternative binding sites using fragment-based approaches. A surface plasmon resonance (SPR) fragment screen designed to detect secondary binding sites in HSP70 led to the identification by X-ray crystallography of a cryptic binding site in the nucleotide-binding domain (NBD) of HSP70 adjacent to the ATP-binding site. Fragment binding was confirmed and characterized as ATP-competitive using SPR and ligand-observed NMR methods. Molecular dynamics simulations were applied to understand the interactions with the protein upon ligand binding, and local secondary structure changes consistent with interconversion between the observed crystal structures with and without the cryptic pocket were detected. A virtual high-throughput screen (vHTS) against the cryptic pocket was conducted, and five compounds with diverse chemical scaffolds were confirmed to bind to HSP70 with micromolar affinity by SPR. These results identified and characterized a new targetable site on HSP70. While targeting HSP70 remains challenging, the new site may provide opportunities to develop allosteric ATP-competitive inhibitors with differentiated physicochemical properties from current series.  相似文献   

3.
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.  相似文献   

4.
The parasitic worm, Schistosoma mansoni, expresses unusual fucosylated glycans in a stage-dependent manner that can be recognized by the human innate immune receptor DC-SIGN, thereby shaping host immune responses. We have developed a synthetic approach for mono- and bis-fucosylated LacdiNAc (LDN-F and LDN-DF, respectively), which are epitopes expressed on glycolipids and glycoproteins of S. mansoni. It is based on the use of monosaccharide building blocks having carefully selected amino-protecting groups, facilitating high yielding and stereoselective glycosylations. The molecular interaction between the synthetic glycans and DC-SIGN was studied by NMR and molecular modeling, which demonstrated that the α1,3-fucoside of LDN-F can coordinate with the Ca2+-ion of the canonical binding site of DC-SIGN allowing for additional interactions with the underlying LDN backbone. The 1,2-fucoside of LDN-DF can be complexed in a similar manner, however, in this binding mode GlcNAc and GalNAc of the LDN backbone are placed away from the protein surface resulting in a substantially lower binding affinity. Glycan microarray binding studies showed that the avidity and selectivity of binding is greatly enhanced when the glycans are presented multivalently, and in this format Lex and LDN-F gave strong responsiveness, whereas no binding was detected for LDN-DF. The data indicates that S. mansoni has developed a strategy to avoid detection by DC-SIGN in a stage-dependent manner by the addition of a fucoside to a number of its ligands.  相似文献   

5.
Efficient cycloaddition of a silylidene‐protected galactal with a suitable heterodiene yielded the basis for a facile diastereoselective route to a glycopeptide‐mimetic scaffold. Its carbohydrate part was further extended by β1–3‐linked galactosylation. The pyranose rings retain their 4C1 chair conformation, as shown by molecular modeling and NMR spectroscopy, and the typical exo‐anomeric geometry was observed for the disaccharide. The expected bioactivity was ascertained by saturation‐transfer‐difference NMR spectroscopy by using the galactoside‐specific plant toxin viscumin as a model lectin. The experimental part was complemented by molecular docking. The described synthetic route and the strategic combination of computational and experimental techniques to reveal conformational properties and bioactivity establish the prepared α‐O‐linked glycopeptide mimetics as promising candidates for further exploitation of this scaffold to give O‐glycans for lectin blocking and vaccination.  相似文献   

6.
Facile prepolymerization and postpolymerization functionalization approaches to prepare well‐defined fluorescent conjugated glycopolymers through Cu(I)‐catalyzed azide/alkyne “Click” ligation were explored. Two well‐defined carbazole‐based fluorescent conjugated glycopolymers were readily synthesized based on these strategies and characterized by 1H NMR, 13C NMR, IR spectra, and UV‐vis spectra. The “Click” ligation offers a very effective conjugation method to covalently attach carbohydrate residues to fluorescent conjugated polymers. In addition, the studies of carbohydrate–lectin interactions were performed by titration of concanavalin A (Con A) to D ‐glucose‐bearing poly(anthracene‐alt‐carbazole) copolymer P‐2 resulting in significant fluorescence quenching of the polymer due to carbohydrate–lectin interactions. When peanut agglutinin (PNA) was added, no distinct change in the fluorescent properties of P‐2 was observed. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2948–2957, 2009  相似文献   

7.
The phosphoryl‐transfer mechanism of shikimate kinase from Mycobacterium tuberculosis and Helicobacter pylori, which is an attractive target for antibiotic drug discovery, has been studied by 1D 1H and 31P NMR spectroscopy. Metaphosphoric acid proved to be a good mimetic of the metaphosphate intermediate and facilitated the ready and rapid evaluation by NMR spectroscopic analysis of a dissociative mechanism. The required closed form of the active site for catalysis was achieved by the use of ADP (product) or two synthetic ADP analogues (AMPNP, AMPCP). Molecular dynamics simulation studies reported here also revealed that the essential arginine (Arg116/Arg117 in H. pylori and M. tuberculosis, respectively), which activates the γ‐phosphate group of ATP for catalysis and triggers the release of the product for turnover, would also be involved in the stabilisation of the metaphosphate intermediate during catalysis. We believe that the studies reported here will be helpful for future structure‐based design of inhibitors of this attractive target. The approach is also expected be useful for studies on the possible dissociative mechanism of other kinase enzymes.  相似文献   

8.
The (+) and ( ? ) enantiomers for a cryptophane-7-bond-linker-benzenesulfonamide biosensor (C7B) were synthesised and their chirality was confirmed by electronic circular dichroism spectroscopy. Biosensor binding to carbonic anhydrase II (CAII) was characterised for both enantiomers by hyperpolarised (HP) 129Xe NMR spectroscopy. Our previous study of the racemic ( ± ) C7B biosensor–CAII complex [Chambers, J.M.; Hill, P.A.; Aaron, J.A.; Han, Z.H.; Christianson, D.W.; Kuzma, N.N.; Dmochowski, I.J. J. Am. Chem. Soc.2009, 131, 563–569] identified two ‘bound’ 129Xe@C7B peaks by HP 129Xe NMR (at 71 and 67 ppm, relative to ‘free’ biosensor at 64 ppm), which led to the initial hypothesis that (+) and ( ? ) enantiomers produce diastereomeric peaks when coordinated to Zn2+ at the chiral CAII active site. Unexpectedly, the single enantiomers complexed with CAII also identified two ‘bound’ 129Xe@C7B peaks: (+) 72, 68 ppm and ( ? ) 68, 67 ppm. These results are consistent with X-ray crystallographic evidence for benzenesulfonamide inhibitors occupying a second site near the CAII surface. As illustrated by our studies of this model protein–ligand interaction, HP 129Xe NMR spectroscopy can be useful for identifying supramolecular assemblies in solution.  相似文献   

9.
Protein mobility in living cells is vital for cell function. Both cytosolic viscosity and weak protein–protein interactions affect mobility, but examining viscosity and weak interaction effects is challenging. Herein, we demonstrate the use of 19F NMR spectroscopy to measure cytoplasmic viscosity and to characterize nonspecific protein–protein interactions in living Escherichia coli cells. The origins of resonance broadening in Escherichia coli cells were also investigated. We found that sample inhomogeneity has a negligible effect on resonance broadening, the cytoplasmic viscosity is only about 2–3 times that of water, and ubiquitous transient weak protein–protein interactions in the cytosol play a significant role in governing the detection of proteins by using in‐cell NMR spectroscopy.  相似文献   

10.
The New Delhi metallo‐β‐lactamase (NDM‐1) is involved in the emerging antibiotic resistance problem. Development of metallo‐β‐lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site‐selective labeling of NDM‐1 with 1,1,1‐trifluoro‐3‐bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using 19F NMR spectroscopy. The results demonstrate different modes of binding of known NDM‐1 inhibitors, including L ‐ and D ‐captopril by monitoring the changing chemical environment of the active‐site loop of NDM‐1. The method described will be applicable to other MBLs and more generally to monitoring ligand‐induced conformational changes.  相似文献   

11.
Hen‐egg‐white lysozyme (HEWL) is specifically cleaved at the Trp28–Val29 and Asn44–Arg45 peptide bonds in the presence of a Keggin‐type [Ce(α‐PW11O39)2]10? polyoxometalate (POM; 1 ) at pH 7.4 and 37 °C. The reactivity of 1 towards a range of dipeptides was also examined and the calculated reaction rates were comparable to those observed for the hydrolysis of HEWL. Experiments with α‐lactalbumin (α‐LA), a protein that is structurally highly homologous to HEWL but has a different surface potential, showed no evidence of hydrolysis, which indicates the importance of electrostatic interactions between 1 and the protein surface for the hydrolytic reaction to occur. A combination of spectroscopic techniques was used to reveal the molecular interactions between HEWL and 1 that lead to hydrolysis. NMR spectroscopy titration experiments showed that on protein addition the intensity of the 31P NMR signal of 1 gradually decreased due to the formation of a large protein/polyoxometalate complex and completely disappeared when the HEWL/ 1 ratio reached 1:2. Circular dichroism (CD) measurements of HEWL indicate that addition of 1 results in a clear decrease in the signal at λ=208 nm, which is attributed to changes in the α‐helical content of the protein. 15N–1H heteronuclear single quantum coherence (HSQC) NMR measurements of HEWL in the presence of 1 reveal that the interaction is mainly observed for residues that are located in close proximity to the first site in the α‐helical part of the structure (Trp28–Val29). The less pronounced NMR spectroscopic shifts around the second cleavage site (Asn44–Arg45), which is found in the β‐strand region of the protein, might be caused by weaker metal‐directed binding, compared with strong POM‐directed binding at the first site.  相似文献   

12.
Concerted functioning of lectins and carbohydrate‐processing enzymes, mainly glycosidases, is essential in maintaining life. It was commonly assumed that the mechanisms by which each class of protein recognizes their cognate sugar partners are intrinsically different: multivalency is a characteristic feature of carbohydrate–lectin interactions, whereas glycosidases bind to their substrates or substrate‐analogue inhibitors in monovalent form. Recent observations on the glycosidase inhibitory potential of multivalent glycomimetics have questioned this paradigm and led to postulate an inhibitory multivalent effect. Here the mechanisms at the origin of this phenomenon have been investigated. A D ‐gluco‐configured sp2‐iminosugar glycomimetic motif, namely 1‐amino‐5N,6O‐oxomethylydenenojirimycin (1N‐ONJ), behaving, simultaneously, as a ligand of peanut agglutinin (PNA) lectin and as an inhibitor of several glycosidases, has been identified. Both the 1N‐ONJ–lectin‐ and 1N‐ONJ–glycosidase‐recognition processes have been found to be sensitive to multivalency, which has been exploited in the design of a lectin–glycosidase competitive assay to explore the implication of catalytic and non‐glycone sites in enzyme binding. A set of isotropic dodecavalent C60‐fullerene–sp2‐iminosugar balls incorporating matching or mismatching motifs towards several glycosidases (inhitopes) was synthesized for that purpose, thereby preventing differences in binding modes arising from orientational preferences. The data supports that: 1) multivalency allows modulating the affinity and selectivity of a given inhitope towards glycosidases; 2) multivalent presentation can switch on the inhibitory capacity for some inhitope–glycosidase pairs, and 3) interactions of the multivalent inhibitors with non‐glycone sites is critical for glycosidase recognition. The ensemble of results point to a shift in the binding mode on going from monovalent to multivalent systems: in the first case a typical ′′key–lock′′ model involving, essentially, the high‐affinity active site can be assumed, whereas in the second, a lectin‐like behavior implying low‐affinity non‐glycone sites probably operates. The differences in responsiveness to multivalency for different glycosidases can then be rationalized in terms of the structure and accessibility of the corresponding carbohydrate‐binding regions.  相似文献   

13.
Metal‐binding scaffolds incorporating a Trp/His‐paired epitope are instrumental in giving novel insights into the physicochemical basis of functional and mechanistic versatility conferred by the Trp–His interplay at a metal site. Herein, by coupling biometal site mimicry and 1H and 13C NMR spectroscopy experiments, modular constructs EDTA‐(L ‐Trp, L ‐His) (EWH; EDTA=ethylenediamino tetraacetic acid) and DTPA‐(L ‐Trp, L ‐His) (DWH; DTPA=diethylenetriamino pentaacetic acid) were employed to dissect the static and transient physicochemical properties of hydrophobic/hydrophilic aromatic interactive modes surrounding biometal centers. The binding feature and identities of the stoichiometric metal‐bound complexes in solution were investigated by using 1H and 13C NMR spectroscopy, which facilitated a cross‐validation of the carboxylate, amide oxygen, and tertiary amino groups as the primary ligands and indole as the secondary ligand, with the imidazole (Im) N3 nitrogen being weakly bound to metals such as Ca2+ owing to a multivalency effect. Surrounding the metal centers, the stereospecific orientation of aromatic rings in the diastereoisomerism is interpreted with the Ca2+–EWH complex. With respect to perturbed Trp side‐chain rotamer heterogeneity, drastically restricted Trp side‐chain flexibility and thus a dynamically constrained rotamer interconversion due to π interactions is evident from the site‐selective 13C NMR spectroscopic signal broadening of the Trp indolyl C3 atom. Furthermore, effects of Trp side‐chain fluctuation on indole/Im orientation were the subject of a 2D NMR spectroscopy study by using the Ca2+‐bound state; a C? H2(indolyl)/C? H5(Im+) connectivity observed in the NOESY spectra captured direct evidence that the N? H1 of the Ca2+–Im+ unit interacted with the pyrrole ring of the indole unit in Ca2+‐bound EWH but not in DWH, which is assignable to a moderately static, anomalous, T‐shaped, interplanar π+–π stacking alignment. Nevertheless, a comparative 13C NMR spectroscopy study of the two homologous scaffolds revealed that the overall response of the indole unit arises predominantly from global attractions between the indole ring and the entire positively charged first coordination sphere. The study thus demonstrates the coordination‐sphere/geometry dependence of the Trp/His side‐chain interplay, and established that π interactions allow 13C NMR spectroscopy to offer a new window for investigating Trp rotamer heterogeneity near metal‐binding centers.  相似文献   

14.
Antagonists of the AT1receptor (AT1R) are beneficial molecules that can prevent the peptide hormone angiotensin II from binding and activating the specific receptor causing hypertension in pathological states. This review article summarizes the multifaced applications of solid and liquid state high resolution nuclear magnetic resonance (NMR) spectroscopy in antihypertensive commercial drugs that act as AT1R antagonists. The 3D architecture of these compounds is explored through 2D NOESY spectroscopy and their interactions with micelles and lipid bilayers are described using solid state 13CP/MAS, 31P and 2H static solid state NMR spectroscopy. Due to their hydrophobic character, AT1R antagonists do not exert their optimum profile on the AT1R. Therefore, various vehicles are explored so as to effectively deliver these molecules to the site of action and to enhance their pharmaceutical efficacy. Cyclodextrins and polymers comprise successful examples of effective drug delivery vehicles, widely used for the delivery of hydrophobic drugs to the active site of the receptor. High resolution NMR spectroscopy provides valuable information on the physical-chemical forces that govern these drug:vehicle interactions, knowledge required to get a deeper understanding on the stability of the formed complexes and therefore the appropriateness and usefulness of the drug delivery system. In addition, it provides valuable information on the rational design towards the synthesis of more stable and efficient drug formulations.  相似文献   

15.
Bacterial production of β-lactamases with carbapenemase activity is a global health threat. The active sites of class D carbapenemases such as OXA-48, which is of major clinical importance, uniquely contain a carbamylated lysine residue which is essential for catalysis. Although there is significant interest in characterizing this post-translational modification, and it is a promising inhibition target, protein carbamylation is challenging to monitor in solution. We report the use of 19F NMR spectroscopy to monitor the carbamylation state of 19F-labelled OXA-48. This method was used to investigate the interactions of OXA-48 with clinically used serine β-lactamase inhibitors, including avibactam and vaborbactam. Crystallographic studies on 19F-labelled OXA-48 provide a structural rationale for the sensitivity of the 19F label to active site interactions. The overall results demonstrate the use of 19F NMR to monitor reversible covalent post-translational modifications.  相似文献   

16.
The synthesis, characterization, and theoretical investigation by means of quantum‐chemical calculations of an oligonuclear metal‐rich compound are presented. The reaction of homoleptic dinuclear palladium compound [Pd2(μ‐GaCp*)3(GaCp*)2] with ZnMe2 resulted in the formation of unprecedented ternary Pd/Ga/Zn compound [Pd2Zn6Ga2(Cp*)5(CH3)3] ( 1 ), which was analyzed by 1H and 13C NMR spectroscopy, MS, elemental analysis, and single‐crystal X‐ray diffraction. Compound 1 consisted of two Cs‐symmetric molecular isomers, as revealed by NMR spectroscopy, at which distinct site‐preferences related to the Ga and Zn positions were observed by quantum‐chemical calculations. Structural characterization of compound 1 showed significantly different coordination environments for both palladium centers. Whilst one Pd atom sat in the central of a bi‐capped trigonal prism, thereby resulting in a formal 18‐valence electron fragment, {Pd(ZnMe)2(ZnCp*)4(GaMe)}, the other Pd atom occupied one capping unit, thereby resulting in a highly unsaturated 12‐valence electron fragment, {Pd(GaCp*)}. The bonding situation, as determined by atoms‐in‐molecules analysis (AIM), NBO partial charges, and molecular orbital (MO) analysis, pointed out that significant Pd? Pd interactions had a large stake in the stabilization of this unusual molecule. The characterization and quantum‐chemical calculations of compound 1 revealed distinct similarities to related M/Zn/Ga Hume–Rothery intermetallic solid‐state compounds, such as Ga/Zn‐exchange reactions, the site‐preferences of the Zn/Ga positions, and direct M? M bonding, which contributes to the overall stability of the metal‐rich compound.  相似文献   

17.
The molecular binding behaviour of the symmetrically substituted tetramethylcucurbit[6]uril (TMeQ[6]) was examined in relationship to the two pyridine-based molecular guests 1,6-hexanedipyridinium dication (Hdipy2+) and the HCl salt of N,N′-bis(3-pyridylmethyl)-diaminoethane (Ediamp). The interactions and binding modes of each guest with TMeQ[6] are discussed using solution results (1H NMR spectroscopy) and solid-state findings (single-crystal X-ray diffraction), to evaluate interactions in common. Supramolecular structures are formed that rely on a combination of the now typical driving forces associated with Q[n] as a molecular host, which are dipole–ion, hydrophobic, H-bonding and in the present examples include π…π and C–H…π interactions.  相似文献   

18.
Cycloaddition of C,N‐diphenylnitrones 1 to N‐aryl maleimides 2 afforded two diastereomeric isoxazolidines with high selectivity. The structure and steric configuration of the adducts have been assigned on the basis of 1H NMR, 1H NMR COSY, 13C NMR and IR spectroscopy. The π–π stacking interactions between maleimide's and nitrone's aromatic rings during the 1,3‐dipolar cycloaddition were assumed to control the exo–endo selectivity of the reaction. Thus, the exo–endo ratio depends upon the position of the substituent present on the C‐phenyl ring of the C,N‐diphenylnitrones.  相似文献   

19.
Three Lewis acid–base adducts t‐Bu3Ga–EPh3 (E = P 1 , As 2 , Sb 3 ) were synthesized by reactions of Ph3E and t‐Bu3Ga and characterized by heteronuclear NMR (1H, 13C (31P)) and IR spectroscopy, elemental analysis and single crystal X‐ray diffraction. Their structural parameters are discussed and compared to similar t‐Bu3Ga adducts. The strength of the donor‐acceptor interactions within 1 – 3 was investigated in solution by temperature‐dependent 1H NMR spectroscopy and by quantum chemical calculations.  相似文献   

20.
A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.  相似文献   

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