Many bacteria regulate gene expression through a cell-cell signaling process called quorum sensing (QS). In proteobacteria, QS is largely mediated by signaling molecules known as N-acylated L-homoserine lactones (AHLs) and their associated intracellular LuxR-type receptors. The design of non-native small molecules capable of inhibiting LuxR-type receptors, and thereby QS, in proteobacteria is an active area of research, and numerous lead compounds are AHL derivatives that mimic native AHL signals. Much of this past work has focused on the pathogen Pseudomonas aeruginosa, which controls an arsenal of virulence factors and biofilm formation through QS. The MexAB-OprM drug efflux pump has been shown to play a role in the secretion of the major AHL signal in P. aeruginosa, N-(3-oxododecanoyl) L-homoserine lactone. In the current study, we show that a variety of non-native AHLs and related derivatives capable of inhibiting LuxR-type receptors in P. aeruginosa display significantly higher potency in a P. aeruginosa Δ(mexAB-oprM) mutant, suggesting that MexAB-OprM also recognizes these compounds as substrates. We also demonstrate that the potency of 5,6-dimethyl-2-aminobenzimidazole, recently shown to be a QS and biofilm inhibitor in P. aeruginosa, is not affected by the presence or absence of the MexAB-OprM pump. These results have implications for the use of non-native AHLs and related derivatives as QS modulators in P. aeruginosa and other bacteria, and provide a potential design strategy for the development of new QS modulators that are resistant to active efflux.
N-acyl l-homoserine lactone; anti-virulence; efflux pump; MexAB-OprM; Pseudomonas aeruginosa; quorum sensing
Structural characterization of DNA-protein crosslinks involving cysteine using reductive desulfurization in combination with liquid chromatography-tandem mass spectrometry is highlighted. The novel approach was used to identify hydrolytically stable DNA-protein lesions involving alkylguanine DNA alkyltransferase (AGT).
DNA-protein crosslinks; O6-alkylguanine DNA alkyltransferase; labile and nonlabile DNA adducts; desulfurization; liquid chromatography-tandem mass spectrometry
α-Conotoxin MII (α-CTxMII) is a 16 amino acid peptide with the sequence GCCSNPVCHLEHSNLC containing disulfide bonds between Cys2-Cys8 and Cys3-Cys16. This peptide, isolated from the venom of the marine cone snail Conus magus, is a potent and selective antagonist of neuronal nicotinic acetylcholine receptors (nAChRs). To evaluate the impact of channel-ligand interactions on ligand binding affinity, homology models of the heteropentameric α3β2-nAChR were constructed. The models were created in MODELLER using crystal structures of the Torpedo marmorata-nAChR (Tm-nAChR, PDB ID: 2BG9) and the Aplysia californica-acetylcholine binding protein (Ac-AChBP, PDB ID: 2BR8) as templates for the α3 and β2 subunit isoforms derived from rat neuronal nAChR primary amino acid sequences. Molecular docking calculations were performed with AutoDock to evaluate interactions of the heteropentameric nAChR homology models with the ligands acetylcholine (ACh) and α-CTxMII. The nAChR homology models described here bind ACh with commensurate binding energies to previously reported systems, and identify critical interactions that facilitate both ACh and α-CTxMII ligand binding. The docking calculations revealed an increased binding affinity of the α3β2-nAChR for α-CTxMII with ACh bound to the receptor, which was confirmed through two-electrode voltage clamp experiments on oocytes from Xenopus laevis. These findings provide insights into the inhibition and mechanism of electrostatically driven antagonist properties of the α-CTxMIIs on nAChRs.
AutoDock; Conotoxin; Homology Modeling; Nicotinic Acetylcholine Receptor; Two-Electrode Voltage Clamp
Multiparametric flow cytometry offers a powerful approach to single cell analysis with broad applications in research and diagnostics. Despite advances in instrumentation, progress in methodology has lagged, offering no simple and efficient method for antibody labeling or quantifying antibody binding per cell. Here, we describe a DNA-directed assembly approach to fluorescent labeling that overcomes these barriers. Oligonucleotide-tagged antibodies and microparticles are annealed to complementary oligonucleotides bearing fluorophores to create assay-specific labeling probes and controls, respectively. The relative fluorescent intensity of labeled cells to control particles allows direct conversion of qualitative data to quantitative units of antibody binding per cell. Importantly, a single antibody can be labeled with any fluor using a simple mix-and-match labeling strategy. Thus, any antibody can provide a quantitative probe in any fluorescent channel, overcoming major barriers that limit the value of flow cytometry as a tool for systems biology and clinical diagnostics.
antibodies; fluorescent probes; immunology; hydrazones; oligonucleotides
The ability to design artificial extracellular matrices as cell instructive scaffolds has opened the door to technologies capable of studying cell fate in vitro and to guide tissue repair in vivo. One main component of the design of artificial extracellular matrices is the incorporation of biochemical cues to guide cell phenotype and multicellular organization. The extracellular matrix is composed of a heterogeneous mixture of proteins that present a variety of spatially discrete signals to residing cell populations. In contrast, most engineered ECMs do not mimic this heterogeneity. In recent years the use of photodeprotection has been used to achieve spatial immobilization of signals. However, these approaches have been limited mostly to small peptides. Here we combine photodeprotection with enzymatic reaction to achieve spatially controlled immobilization of active bioactive signals that range from small molecules to large proteins. A peptide substrate for transglutaminase factor XIII (FXIIIa) is caged with a photodeprotectable group, which is then immobilized to the bulk of a cell compatible hydrogel. With the use of focused light the substrate can be deprotected and used to immobilize patterned bioactive signals. This approach offers an innovative strategy to immobilize delicate bioactive signals, such as growth factors, without loss of activity and enables In situ cell manipulation of encapsulated cells.
Photopatterning; enzymatic reaction; hydrogels; ortho-nitrobenzyl; Factor XIIIa
Monosaccharide lipid A mimetics composed by a glucosamine core linked to two fatty acid chains and bearing one or two phosphates have been synthesized. While compounds 1 and 2, with one phosphate group, were practically inactive in inhibiting LPS-induced TLR4 signaling and cytokine production in HEK-blue™ cells and murine macrophages, compound 3 with two phosphates was found to be active in efficiently inhibiting TLR4 signal in both cell types. The direct interaction of molecule 3 with MD-2 co-receptor has been investigated by means of NMR and molecular modeling/docking analysis. This compound also interacts directly with CD14 receptor, stimulating its internalization by endocytosis. Experiments on macrophages show that the effect on CD14 reinforces the activity on MD-2.TLR4, because compound 3 activity is higher when CD14 is important for TLR4 signaling i,e, at low LPS concentration. The dual MD-2 and CD14 targeting, accompanied by good solubility in water and lack of toxicity, suggests the use of monosaccharide 3 as a lead compound to develop drugs directed against TLR4-related syndromes.
drugs; carbohydrates; bioorganic chemistry; NMR; molecular modeling
differential receptor; SNP analysis; dumbbell molecular beacon; principal component analysis
Nearly 50 naturally-occurring carbapenem β-lactam antibiotics, most produced by Streptomyces, have been identified. The structural diversity of these compounds is limited to variance of the C-2 and C-6 side chains as well as the stereochemistry at C-5/C-6. These structural motifs are of interest both for their antibiotic effects and their biosynthesis. While the thienamycin gene cluster is the only active gene cluster publically available in this group, more comparative information is needed to understand the genetic basis of these structural differences. We report here the identification of MM 4550, a member of the olivanic acids, as the major carbapenem produced by S. argenteolus ATCC 11009. Its gene cluster was also identified by degenerate PCR and targeted gene inactivation. Sequence analysis revealed that genes encoding the biosynthesis of the bicyclic core and the C-6 and C-2 side chains are well conserved in the MM 4550 and thienamycin gene clusters. Three new genes, cmmSu, cmm17 and cmmPah were found in the new cluster and their putative functions in the sulfonation and epimerization of MM 4550 are proposed. Gene inactivation showed that, in addition to cmmI, two new genes, cmm22/23, encode a two-component response system thought to regulate the production of MM 4550. Overexpression of cmmI, cmm22 and cmm23 promoted MM 4550 production in an engineered strain. Finally, the involvement and putative roles of all genes in the MM 4550 cluster are proposed based on the results of bioinformatics analysis, gene inactivation, and analysis of disruption mutants. Overall, the differences between the thienamycin and MM 4550 gene clusters are reflected in characteristic structural elements and provide new insights into the biosynthesis of the complex carbapenems.
β-lactams; carbapenems; biosynthesis; MM 4550; Streptomyces argenteolus
Strain-promoted azide-alkyne cycloaddition (SPAAC) can be used to generate artificial metalloenzymes (ArMs) from scaffold proteins containing a p-azido-L-phenylalanine (Az) residue and catalytically active bicyclononyne-substituted metal complexes. The high efficiency of this reaction allows rapid ArM formation using Az residues within the scaffold protein in the presence of cysteine residues or various reactive components of cellular lysate. In general, cofactor-based ArM formation allows the use of any desired metal complex to build unique inorganic-protein materials. SPAAC covalent linkage further decouples the native function of the scaffold from the installation process since it is not affected by native amino acid residues; as long as an Az residue can be incorporated, an ArM can be generated. We have demonstrated the scope of this method with respect to both the scaffold and cofactor components and established that the dirhodium ArMs generated can catalyze the decomposition of diazo compounds and both Si-H and olefin insertion reactions involving these carbene precursors.
artificial metalloenzyme; biocatalysis; cofactor; click chemistry; dirhodium
bifacial; nucleobase mimic; bPNA; hairpin; triplex
Quorum sensing (QS) is a process by which bacteria use low molecular weight signaling molecules (or autoinducers) to assess their local population densities and alter gene expression levels at high cell numbers. Many Gram-negative bacteria use N-acyl L-homoserine lactones (AHLs) with aliphatic acyl groups as signaling molecules for QS. However, bacteria that utilize AHLs with aroyl acyl groups have been recently discovered, including the metabolically versatile soil bacterium Rhodopseudomonas palustris, which uses p-coumaroyl HL (p-cAHL) as its QS signal. This autoinducer is especially unusual because its acyl group is believed to originate from a monolignol (i.e., p-coumarate) produced exogenously by plants in the R. palustris environment, rather than through the endogenous fatty acid biosynthesis pathway like other native AHLs. As such, p-cAHL could signal not only bacterial density but also the availability of an exogenous plant-derived substrate, and may even constitute an interkingdom signal. Similar to other Gram-negative bacteria, QS in R. palustris is controlled by the p-cAHL signal binding its cognate LuxR-type receptor, RpaR. We sought to determine if non-native aroyl HLs (ArHLs) could potentially activate or inhibit RpaR in R. palustris, and thereby modulate QS in this soil bacterium. Herein, we report the testing of a set of synthetic ArHLs for RpaR agonism and antagonism using a R. palustris reporter strain. Several potent non-native RpaR agonists and antagonists were identified. Additionally, the screening data revealed that lower concentrations of ArHL are required to strongly agonize RpaR relative to antagonizing RpaR. Structure-activity relationship (SAR) analyses of the active ArHLs indicated that potent RpaR agonists tend to have sterically small substituents on their aryl groups, most notably in the ortho position. In turn, the strong RpaR antagonists were based on either the phenylpropionyl HL (PPHL) or the phenoxyacetyl HL (POHL) scaffold, and many contained an electron-withdrawing group at either the meta or para positions of the aryl ring. To our knowledge, the compounds reported herein represent the first abiotic chemical modulators of RpaR, and more generally, the first abiotic ligands capable of intercepting QS in bacteria that utilize native ArHL signals. In view of the novel origins of the p-cAHL signal in R. palustris, the largely unknown role of QS in this bacterium, and R. palustris’ unique environmental lifestyles, we anticipate that these compounds could be valuable as chemical probes to study QS in R. palustris in a range of fundamental and applied contexts.
N-Acyl homoserine lactone; Bacteria; Cell-cell signaling; LuxR-type receptor; Quorum sensing; Rhodopseudomonas palustris; RpaR
Multidrug resistance (MDR) caused by ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) through extrusion of anticancer drugs from the cells is a major cause of failure to cancer chemotherapy. Previously, selenazole containing cyclic peptides were reported as P-gp inhibitors and these were also used for co-crystallization with mouse P-gp, which has 87% homology to human P-gp. It has been reported that human P-gp, can simultaneously accommodate 2-3 moderate size molecules at the drug binding pocket. Our in-silico analysis based on the homology model of human P-gp spurred our efforts to investigate the optimal size of (S)-valine-derived thiazole units that can be accommodated at drug-binding pocket. Towards this goal, we synthesized varying lengths of linear and cyclic derivatives of (S)-valine-derived thiazole units to investigate the optimal size, lipophilicity and the structural form (linear and cyclic) of valine-derived thiazole peptides that can accommodate well in the P-gp binding pocket and affects its activity, previously an unexplored concept. Among these oligomers, lipophilic linear- (13) and cyclic-trimer (17) derivatives of QZ59S-SSS were found to be the most and equally potent inhibitors of human P-gp (IC50 = 1.5 μM). Cyclic trimer and linear trimer being equipotent, future studies can be focused on non-cyclic counterparts of cyclic peptides maintaining linear trimer length. Binding model of the linear trimer (13) within the drug-binding site on the homology model of human P-gp represents an opportunity for future optimization, specifically replacing valine and thiazole groups in the non-cyclic form.
ABC transporter; P-glycoprotein; molecular modeling; multidrug resistance; peptide mimics
Heterocyclic diamidines are strong DNA minor groove binders and have excellent antiparasitic activity. To extend the biological activity of these compounds, a series of arylimidamides (AIAs) analogs, which have better uptake properties in Leishmania and T. cruizi than diamidines, was prepared. The binding of the AIAs to DNA was investigated by Tm, fluorescence displacement titration, circular dichroism, DNase I footprinting, biosensor surface plasmon resonance, X-ray Crystallography and molecular modeling. These compounds form 1:1 complexes with AT sequences in the DNA minor groove and the binding strength varies with substituent size, charge and polarity. This substituent dependent structure and properties provide a SAR that can be used to estimate K values for binding to DNA in this series. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for AIAs.
Arylimidamides (AIAs); DNA; Minor Groove Binder; Molecular Modeling; X-ray Crystallography
strain-promoted alkyne-azide cycloaddition; sortase A-mediated ligation; one-pot; PEGylation; fluorescent labeling; thrombomodulin
Guanine nucleotide (G)-protein coupled receptor (GPCR) linked cell signaling cascades are initiated upon binding of a specific agonist ligand to its cell surface receptor. Linking multiple heterologous ligands that simultaneously bind and potentially cross-link different receptors on the cell surface is a unique approach to modulate cell responses. Moreover, if the target receptors are pre-selected, based on analysis of cell specific expression of a receptor combination, then the linked binding elements may provide enhanced specificity of targeting to the cell type of interest; i.e., only to cells that express the complementary receptors. Two receptors whose expression is relatively specific, as a combination, to the insulin secreting β-cell of the pancreas, are the sulfonylurea-1 (SUR1) and the glucagon-like peptide-1 (GLP-1) receptors. A heterobivalent ligand was assembled of the active fragment of GLP-1 ([Phe12, Arg36] 7-36 GLP-1) and glibenclamide,a small organic ligand to the SUR1. The synthetic construct was labelled with Cy5 or Europium chelated in DTPA to evaluate binding to β-cell lines using fluorescence microscopy or time-resolved saturation and competition binding assays, respectively. Once the ligand binds to β-cells, it is rapidly capped and presumably removed from the cell surface via endocytosis. The bivalent ligand had an affinity ~3 fold higher than monomeric Europium labelled GLP-1, likely due to cooperative binding to the complimentary receptors on the βTC3 cells. The high affinity binding was lost in the presence of either unlabelled monomer demonstrating that interaction with both receptors is required for the enhanced binding at low concentrations. Importantly, bivalent enhancement was accomplished in a cell system with physiological levels of expression of the complementary receptors, indicating that this approach may be applicable for β-cell targeting in vivo.
binding assay; lanthanide-based time-resolved fluorescence; molecular dynamics; peptidomimetics; solid-phase synthesis
Basidiomycota represent a diverse source of natural products, particularly the sesquiterpenoids. Recently, the genome sequencing, mining, and subsequent discovery of a suite of sesquiterpene synthases was described in Omphalotus olearius. A predictive framework was developed to facilitate the discovery of sesquiterpene synthases in Basidiomycota. Phylogenetic analyses indicated a conservation of both sequence and initial cyclization mechanisms used. Here, the first robust application of this predictive framework is reported. It is used to pursue and selectively identify sesquiterpene synthases that follow a 1,6-, 1,10-, and 1,11-cyclization mechanism in the crust fungus Stereum hirsutum. The successful identification and characterization of a 1,6- and a 1,10-cyclizing sesquiterpene synthase, as well as three 1,11-cyclizing Δ-6 protoilludene synthases, is described. This study verifies the accuracy and utility of the predictive framework as a roadmap for the discovery of specific sesquiterpene synthases from Basidiomycota, representing an important step forward in natural product discovery.
kinetics; anticancer agents; biosynthesis; natural products; GC/MS
Dystroglycanopathies are a subgroup of muscular dystrophies that arise from defects in the enzymes implicated in the recently elucidated O-mannosylation pathway, resulting in underglycosylation of α-dystroglycan. The emerging identification of additional brain proteins modified by O-mannosylation provides a broader context for interpreting the range of neurological consequences associated with dystroglycanopathies. This form of glycosylation is associated with protein mucin-like domains which present numerous serine and threonine residues as possible sites for modification. Further, the O-Man glycans coexist in this region with O-GalNAc glycans, conventionally associated with such protein sequences, resulting in a complex glycoconjugate landscape. Sorting out the relationships between the various molecular defects in glycosylation and the modes of disease presentation, as well as the regulatory interplay among the O-Man glycans, and the effects on other modes of glycosylation in the same domain is challenging. Here we provide a perspective on chemical biology approaches employing synthetic and analytical methods to address these questions.
Glycopeptides; Carbohydrates; Muscular Dystrophy; α-Dystroglycan; Dystroglycanopathy; Protein O-Mannosylation
Herein, a combination of microcontact printing of functionalized alkanethiols and site-specific modification of proteins is utilized to chemoselectively immobilize proteins onto gold surfaces either by oxime or copper catalyzed alkyne-azide click chemistry. Two molecules capable of click reactions, an aminooxy-functionalized alkanethiol and an azide-functionalized alkanethiol, were synthesized, and self-assembled monolayer (SAM) formation on gold was confirmed by IR spectroscopy. The alkanethiols were then individually patterned onto gold surfaces by microcontact printing. Site-specifically modified proteins, horse heart myoglobin (HHMb) containing an N-terminal α-oxoamide and a red-fluorescent protein (mCherry-CVIA) with a C-terminal alkyne, respectively were immobilized by incubation onto the stamped functionalized alkanethiol patterns. Pattern formation was confirmed by fluorescence microscopy.
chemoselectivity; click chemistry; self-assembly; protein immobilization; microcontact printing
Glucose transporters and the glycolysis enzyme lactate dehydrogenase A
(LDH-A) are both overexpressed in cancer cells, two proliferation tactics that
underlie the phenomenon known as the Warburg effect. Herein we report the
development and activity of a glucose-conjugated LDH-A inhibitor designed to
target both of these tumor-promoting facets. In addition to the promise of this
conjugate, dual targeting of the Warburg effect using glycoconjugation as an
anticancer strategy could be applied to inhibitors of many of the enzymes
involved in glycolysis or tumor metabolism.
Warburg effect; glycoconjugation; targeted anticancer agents; drug delivery; cancer
binary deoxyribozyme; peroxidise; visual assay; Mycobacterium tuberculosis; point of care diagnostic
Antibiotics; Polymyxins; Colistin; RNA; Translation
Bacterial biofilms pose a significant challenge in clinical environments due to their inherent lack of susceptibility to antibiotic treatment. It is widely recognized that most pathogenic bacterial strains in the clinical setting persist in the biofilm state, and are the root cause of many recrudescent infections. Discovery and development of compounds capable of either inhibiting biofilm formation or initiating biofilm dispersal may provide new therapeutic avenues for reducing the number of hospital acquired, biofilm-mediated infections. We now report the application of our recently reported image-based, high-throughput screen to the discovery of microbially-derived natural products with biofilm inhibitory activity against Vibrio cholerae. Examination of a prefractionated library of microbially-derived marine natural products has lead to the identification of a new biofilm inhibitor that is structurally unrelated to previously reported inhibitors and is one of the most potent inhibitors reported to date against V. cholerae. Combination of this compound with sub-MIC concentrations of a number of clinically relevant antibiotics was shown to improve the biofilm inhibitory efficacy of this new compound compared to monotherapy treatments, and provides evidence for the potential therapeutic benefit of biofilm inhibitors in treating persistent biofilm-mediated infections.
biofilm inhibitor; drug discovery; Vibrio cholerae. natural products; image-based screening
A recently discovered cause of resistance of tuberculosis to a drug of last resort, the aminoglycoside kanamycin, is modification of this drug by the enhanced intracellular survival (Eis) protein. Eis is a structurally and functionally unique acetyltransferase with an unusual capability of acetylating aminoglycosides at multiple positions. The extent of this regioversatility and its defining protein features are unclear. Herein, we determined the positions and order of acetylation of five aminoglycosides by NMR spectroscopy. This analysis revealed unprecedented acetylation of the 3"-amine of kanamycin, amikacin, and tobramycin, and γ-amine of the 4-amino-2-hydroxybutyryl group of amikacin. A crystal structure of Eis in complex with coenzyme A and tobramycin revealed how tobramycin can be accommodated in the Eis active site in two binding modes consistent with its di-acetylation. These studies describing chemical and structural details of acetylation will guide future efforts towards designing aminoglycosides and Eis inhibitors to overcome resistance in tuberculosis.
Bacterial resistance; Enhanced intracellular survival protein; Enzymatic reaction; Multi-acetylation; Tuberculosis
Unnatural amino acids (Uaas) containing conjugated ring systems are of particular interest for their optical properties. Until now, such structurally bulky and planar Uaas could not be incorporated into proteins using the pyrrolsyl tRNA/synthetase shuttling system. By building a highly diverse synthetase library using the "small intelligent" approach, we evolved novel synthetases specific for two such Uaas and incorporated them into proteins in E. coli and mammalian cells.
unnatural amino acid; pyrrolysine; genetic code expansion; small intelligent library; directed evolution
CREB; inhibitors; protein complementation; protein–protein interactions; transcription