Intrinsic Affinity Research Articles

Intrinsic affinity of acid-activated bentonite towards hydrogen and carbon dioxide

The effect of acid activation on bentonite affinity toward carbon dioxide (CO2) and hydrogen (H2) was investigated at ambient conditions. Characterization through X-ray diffraction and fluorescence, thermal gravimetric analysis, nitrogen adsorption-desorption isotherms, Fourier Transform Infrared spectroscopy and differential scanning calorimetry allowed correlating newly induced textural and structural features with adsorptive properties. Optimum acid treatment improved the specific surface area and porosity. The resulting decrease in dehydration temperature indicates decay in hydrophilic character. The affinity improvement towards hydrogen was due to Brønsted acidity suppression and surface basicity attenuation, which are essential requirements for adsorption on aluminosilicates (AS) via weak Lewis Acid-Base interactions, but excessive acid attack was detrimental. Low Si/Al surfaces should be suitable for CO2 capture, while moderately acid-treated clays should be interesting candidates as hydrogen adsorbents. This allows envisaging promising prospects for low-cost AS-based materials intended for selective CO2-free capture and storage of hydrogen without energy and safety constraints.

Biominerized gold-Hemin@MOF composites with peroxidase-like and gold catalysis activities: A high-throughput colorimetric immunoassay for alpha-fetoprotein in blood by ELISA and gold-catalytic silver staining

Catalytic hemin was first remolded with biomineralized gold to form Hemin-Au core and further encapsulated into the Tb metal organic framework (MOF) matrix. The so obtained Hemin-Au@MOF composites could possess high environmental stability and especially double catalysis activities of enhanced peroxidase-like and gold catalysis. Steady state kinetics studies indicate that Hemin-Au@MOF could present much higher intrinsic catalysis and substrate affinity (lower Michaelis constants) than native hemin and even natural peroxidase. Furthermore, the catalytic composites were employed for labeling antibodies towards the sandwiched immunoassays for alpha-fetoprotein (AFP) as a model biomarker of cancers. The results indicate that the Hemin-Au@MOF-based immunoassays could be conducted by two signal amplification ways of hemin-catalyzed chromogenic reaction and gold-catalyzed silver staining, enabling the detection of AFP in blood with the level down to 0.020 ng mL−1. Importantly, the proposed fabrication protocol combining the gold biomineralization and MOF encapsulation routes may be extended for the fabrication of a variety of enzymes or enzymatic mimics with the improved environmental stability and multiple catalysis activities for the wide catalysis applications.

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.

General regulatory factors (GRFs), such as Reb1, Abf1, Rap1, Mcm1, and Cbf1, positionally organize yeast chromatin through interactions with a core consensus DNA sequence. It is assumed that sequence recognition via direct base readout suffices for specificity and that spurious nonfunctional sites are rendered inaccessible by chromatin. We tested these assumptions through genome-wide mapping of GRFs in vivo and in purified biochemical systems at near–base pair (bp) resolution using several ChIP-exo–based assays. We find that computationally predicted DNA shape features (e.g., minor groove width, helix twist, base roll, and propeller twist) that are not defined by a unique consensus sequence are embedded in the nonunique portions of GRF motifs and contribute critically to sequence-specific binding. This dual source specificity occurs at GRF sites in promoter regions where chromatin organization starts. Outside of promoter regions, strong consensus sites lack the shape component and consequently lack an intrinsic ability to bind cognate GRFs, without regard to influences from chromatin. However, sites having a weak consensus and low intrinsic affinity do exist in these regions but are rendered inaccessible in a chromatin environment. Thus, GRF site-specificity is achieved through integration of favorable DNA sequence and shape readouts in promoter regions and by chromatin-based exclusion from fortuitous weak sites within gene bodies. This study further revealed a severe G/C nucleotide cross-linking selectivity inherent in all formaldehyde-based ChIP assays, which includes ChIP-seq. However, for most tested proteins, G/C selectivity did not appreciably affect binding site detection, although it does place limits on the quantitativeness of occupancy levels.

An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment.

DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified systematic evolution of ligands by exponential enrichment (SELEX) approach. Two Taq-specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls to Taq were identified. TaqI contained 8 nucleotides (5'-CACTAAAG-3') that matched the phage T3 RNAP "core" promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCRs. Similarly, exonuclease- Klenow polymerase also selected a high-affinity primer that contained a related core promoter sequence from phage T7 RNAP (5'-ACTATAG-3'). For both Taq and Klenow, even small modifications to the sequence resulted in large losses in binding affinity, suggesting that binding was highly sequence specific. The results are discussed in the context of possible effects on multiprimer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs.IMPORTANCE This work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function or be a consequence of the structural architecture of the enzyme. New sequence specificity for Taq and Klenow polymerases were uncovered, and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promoters. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology.

Thiazole-substituted benzenesulfonamides as inhibitors of 12 human carbonic anhydrases

Four series of para or meta - substituted thiazolylbenzenesulfonamides bearing Cl substituents were designed, synthesized, and evaluated as inhibitors of all 12 catalytically active recombinant human carbonic anhydrase (CA) isoforms. Observed affinities were determined by the fluorescent thermal shift assay and the intrinsic affinities were calculated based on the fractions of binding-ready deprotonated sulfonamide and CA bearing protonated hydroxide bound to the catalytic Zn(II) in the active site. Several compounds exhibited selectivity towards CA IX, an anticancer target. Intrinsic affinities reached 30 pM, while the observed affinities - 70 nM. The structure-intrinsic affinity relationship map of the compounds showed the energetic contributions of the thiazole ring and its substituents.

Overexpression of ghr-miR166b generates resistance against Bemisia tabaci infestation in Gossypium hirsutum plants.

In silico identified Gossypium hirsutum ghr-miR166b shows multi-compatible targets in mitochondrial ATP synthase of Bemisia tabaci. Its overexpression in planta has the potential to act as a biopesticide in reducing B. tabaci population, and consequently the spread of whitefly-transmitted plant viruses. Whiteflies (B. tabaci) are hemipterous insects that act as a vector to transmit plant viruses causing enormous losses to the plants. In the present study, G. hirsutum-encoded miRNAs targeting expressed sequence tags (ESTs) of B. tabaci, based on sequence complimentarity and miRNA-target mRNA thermodynamics, were in silico identified. Out of 108 G. hirsutum miRNAs, 55 targeted the protein encoding ESTs. Among them, ghr-miR166b was selected owing to its intrinsic affinity for ATP synthase. Its functional role was validated following expression of ghr-MIR166b (precursor) sequence in G. hirsutum cv. HS6 plants through Agrobacterium-mediated transformation. Total of seven independent transformed (T0) G. hirsutum lines were obtained. The transcript level of ghr-MIR166b in the transgenic lines was observed to be 2.0- to 17-fold higher as compared to non-transformed plants. Northern-blot analysis of small RNAs isolated from the transgenic plants confirmed the presence of the ghr-miR166b. After feeding on the leaves of transgenic line (HS6-166-30) having highest level of ghr-miR166b expression, B. tabaci population was reduced up to 91% as compared to non-transformed leaves. Further, in the whole plant assay, a maximum of 78% B. tabaci mortality was observed in the same line, while there was an increase in B. tabaci population on the non-transformed plants. Our results revealed that ghr-miR166b supposedly targeting ATP synthase gene of B. tabaci, and subsequently its overexpression in planta has potential to act as biopesticide for reducing B. tabaci population and consequently spread of whitefly transmitted viruses.

A Genetically Encoded Toolbox of Orthogonal Adhesins for Bacterial Self-Assembly

In over a decade, synthetic biology has developed increasingly robust gene networks within single cells, but constructed very few systems that demonstrate multicellular spatio-temporal dynamics. In particular, to our knowledge there exists no convenient method for engineering cell-cell adhesion. Towards filling this gap in synthetic biology's toolbox, here we report the first 100% genetically encoded self-assembly platform, based on modular cell-cell adhesion in the bacterium Escherichia coli. In this system, adhesive selectivity is provided by a library of outer membrane-displayed peptides with orthogonal intra-library specificities, while affinity is provided by intrinsic adhesin affinity, media conditions, and inducible expression across the entire library. We demonstrate this tool by building a variety of well-defined multicellular patterns, including multiple cell types in cluster-, mesh-, and lattice-like arrangements and comparing these to a biophysical model. This orthogonal, composable adhesion system will enable future development of synthetic multicellular systems for use in consortia-based metabolic engineering, in living materials, in tissue engineering, and in controlled study of minimal multicellular systems.

Improving the water resistance of nanocellulose-based films with polyhydroxyalkanoates processed by the electrospinning coating technique

Polyhydroxyalkanoates (PHAs) comprise a family of biodegradable aliphatic polyesters with enhanced sustainable profile and high water vapor barrier. As environmentally friendly materials, nanostructured cellulose-based films, also called nanopapers, such as films made of cellulose nanofibrils (CNFs) and lignocellulose nanofibrils (LCNFs), are also of growing interest due to their high mechanical strength and outstanding oxygen barrier properties at dry conditions. Unfortunately, nanopapers are highly hydrophilic, lacking of sufficient moisture resistance for uses in, for instance, food packaging. The present study reports, for the first time, on the effect of electrospun poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) double side coatings on the morphology, water contact angle, mechanical properties, and barrier performance of CNF and LCNF films. The resultant multilayer structures showed significantly improved water contact resistance, more balanced mechanical properties, and higher barrier performance against water vapor in comparison to the neat nanopapers. Although the PHA-coated nanopapers presented slightly lower aroma barrier due to the intrinsic affinity of PHA for limonene uptake, these sustainable multilayer films further improved the oxygen performance of the nanopapers, showing significant potential as barrier materials even at high humidity conditions. As a result, the here-developed novel films, based on nanopapers double side coated with electrospun PHB and PHBV layers, appear as a very promising fully bio-based material concept for food packaging applications due to their outstanding water vapor and oxygen barrier performance.

Altered hemoglobin co-factor sensitivity does not underlie the evolution of derived fossorial specializations in the family Talpidae.

The high O2 affinity of European mole (Talpa europaea) blood is postulated to largely arise from the presence of two β-globin chain residues (β4 Ser and β5 Gly) that weaken the interaction of its hemoglobin (Hb) with the red cell organophosphate 2,3-diphosphoglycerate (DPG). This latter trait is generally accepted to be an 'adaptation to subterranean life', despite the fact that no data are available for more basal mole lineages that have no evolutionary history of fossoriality (i.e. the ambulatory, high-elevation shrew-like moles and the semi-aquatic desmans), and which may similarly benefit from an elevated blood O2 affinity. To test whether evolution of a low DPG sensitivity phenotype is linked to derived fossorial lifestyles or represents an ancestral trait for the family, we determined the globin gene sequences and measured the intrinsic O2 affinity and co-factor sensitivity of the major Hb component of the gracile shrew-like mole (Uropsilus gracilis) and the Pyrenean desman (Galemys pyrenaicus). Our results unequivocally demonstrate that the presence of β4 Ser and β5 Gly, together with a low DPG sensitivity Hb phenotype, predates the radiation of the family Talpidae, and hence did not evolve as a specific adaptation to fossorial life. By contrast, our comparative analyses suggest that variations in whole blood O2 affinity among members of this family predominantly arose from amino acid substitutions that increase or decrease the intrinsic O2 affinity of the protein.

Development and evaluation of a CEACAM6-targeting theranostic nanomedicine for photoacoustic-based diagnosis and chemotherapy of metastatic cancer.

Metastasis is the leading cause of cancer-related deaths. A number of chemotherapeutic and early diagnosis strategies, including nanomedicine, have been developed to target metastatic tumor cells. However, simultaneous inhibition and imaging of metastasis is yet to be fully achieved.Methods: To overcome this limitation, we have developed human serum albumin-based nanoparticles (tHSA-NPs) with photoacoustic imaging capability, which target carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6). CEACAM6 is highly expressed in metastatic anoikis-resistant tumor cells.Results: In vitro, the CEACAM6-targeting tHSA-NPs efficiently targeted CEACAM6-overexpressing metastatic anoikis-resistant tumor cells. In vivo, CEACAM6-targeting tHSA-NPs administered intravenously to BALB/c nude mice efficiently inhibited lung metastasis in circulating anoikis-resistant tumor cells compared to the controls. In addition, anoikis-resistant tumor cells can be successfully detected by photoacoustic imaging, both in vitro and in vivo, using the intrinsic indocyanine green-binding affinity of albumin.Conclusion: In summary, the CEACAM6-targeting albumin-based nanoparticles allowed the delivery of drugs and photoacoustic imaging to metastatic anoikis-resistant tumor cells in vitro and in vivo. Based on the expression of CEACAM6 in a variety of tumors, CEACAM6-targeting nanomedicine might be used to target various types of metastatic tumor cells.

A Synthetic Cell-Cell Adhesion Toolbox for Programming Multicellular Morphologies and Patterns

Synthetic multicellular systems hold promise for understanding natural development of biofilms and higher organisms, as well as for engineering complex multi-component metabolic pathways and materials. However, such efforts require tools to adhere cells into defined morphologies and patterns, and these tools are currently lacking. Here we report the first 100% genetically encoded synthetic platform for modular cell-cell adhesion in Escherichia coli, which provides control over multicellular self-assembly. Adhesive selectivity is provided by a library of outer membrane-displayed nanobody and antigen peptides with orthogonal intra-library specificities, while affinity is controlled by intrinsic adhesin affinity, competitive inhibition, and inducible expression. We demonstrate the resulting capabilities for quantitative rational design of well-defined morphologies and patterns through homophilic and heterophilic interactions, lattice-like self-assembly, phase separation, differential adhesion, and sequential layering. This adhesion toolbox, compatible with synthetic biology standards, will enable construction of high-level multicellular designs and shed light on the evolutionary transition to multicellularity.

La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region.

Cell growth is a complex process shaped by extensive and coordinated changes in gene expression. Among these is the tightly regulated translation of a family of growth-related mRNAs defined by a 5′ terminal oligopyrimidine (TOP) motif. TOP mRNA translation is partly controlled via the eukaryotic initiation factor 4F (eIF4F), a translation factor that recognizes the mRNA 5′ cap structure. Recent studies have also implicated La-related protein 1 (LARP1), which competes with eIF4F for binding to mRNA 5′ ends. However, it has remained controversial whether LARP1 represses TOP mRNA translation directly and, if so, what features define its mRNA targets. Here, we show that the C-terminal half of LARP1 is necessary and sufficient to control TOP mRNA translation in cells. This fragment contains the DM15 cap-binding domain as well as an adjacent regulatory region that we identified. We further demonstrate that purified LARP1 represses TOP mRNA translation in vitro through the combined recognition of both the TOP sequence and cap structure, and that its intrinsic repressive activity and affinity for these features are subject to regulation. These results support a model whereby the translation of TOP mRNAs is controlled by a growth-regulated competition between eIF4F and LARP1 for their 5′ ends.

General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.

Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity (KD of >1 mM) and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher affinity (KD of ∼10 μM) for isolated capsid subunits. Therefore, it has been argued that TRIMCyp proteins have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition.IMPORTANCE Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits much more tightly through its cyclophilin A domain and therefore was thought to act independently of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction.

A Bifunctional Perovskite Promoter for Polysulfide Regulation toward Stable Lithium-Sulfur Batteries.

Lithium-sulfur (LiS) batteries are strongly considered as the next-generation rechargeable cells. However, both the shuttle of lithium polysulfides (LiPSs) and sluggish kinetics in random deposition of lithium sulfides (Li2 S) significantly degrade the capacity, rate performance, and cycling life of LiS cells. Herein, bifunctional Ba0.5 Sr0.5 Co0.8 Fe0.2 O3-δ perovskite nanoparticles (PrNPs) are proposed as a promoter to immobilize LiPSs and guide the deposition of Li2 S in a LiS cell. The oxygen vacancy in PrNPs increases the metal reactivity to anchor LiPSs, and co-existence of lithiophilic (O) and sulfiphilic (Sr) sites in PrNP favor the dual-bonding (LiO and SrS bonds) to anchor LiPSs. The high catalytic nature of PrNP facilitates the kinetics of LiPS redox reaction. The PrNP with intrinsic LiPS affinity serves as nucleation sites for Li2 S deposition and guides its uniform propagation. Therefore, the bifunctional LiPS promoter in LiS cell yields high rate performance and ultralow capacity decay rate of 0.062% (a quarter of pristine LiS cells). The proposed strategy to immobilize LiPSs, promotes the conversion of LiPS, and regulates deposition of Li2 S by an emerging perovskite promoter and is also expected to be applied in other energy conversion and storage devices based on multi-electron redox reactions.

Ruthenium(II)–arene complexes of diimines: Effect of diimine intercalation and hydrophobicity on DNA and protein binding and cytotoxicity

A series of half‐sandwich Ru(II)–arene complexes [Ru(η6‐benzene)(diimine)Cl](PF6) (1–4), where diimine is 1,10‐phenanthroline (1), 5,6‐dimethyl‐1,10‐phenanthroline (2), dipyrido[3,2‐a:2′,3′‐c]phenazine (3) or 11,12‐dimethyldipyrido[3,2‐a:2′,3′‐c]phenazine (4), have been isolated and characterized using analytical and spectral methods. Complex 2 possesses a familiar pseudo‐octahedral ‘piano‐stool’ structure. The intrinsic DNA binding affinity of the complexes depends upon the diimine ligand: 3 (dppz) > 4 (11,12‐dmdppz) > 2 (5,6‐dmp) > 1 (phen). The π‐stacking interaction of extended planar ring of coordinated dppz (3) in between the DNA base pairs is more intimate than that of phen (1), and the incorporation of methyl groups on the dppz ring (4) discourages the stacking interaction leading to a lower DNA binding affinity for 4 than 3. Docking studies show that all the complexes bind in the major groove of DNA. Interestingly, 3 shows an ability to convert supercoiled DNA into nicked circular DNA even at 20 μM concentration beyond which complete oxidative DNA degradation is observed. The protein binding affinity of the complexes decreases in the order 4 > 3 > 2 > 1, and the higher protein binding affinity of 4 illustrates the strong involvement of methyl groups on dppz ring in hydrophobic interaction with protein. Also, 4 cleaves protein more efficiently than the other complexes in the presence of H2O2. It is notable that 2, 3 and 4 display cytotoxicity against human cervical cancer cell lines (SiHa) with potency higher than the currently used drug cisplatin. Acridine orange/ethidium bromide staining studies reveal that 3 induces apoptosis in cancer cells much more efficiently than 4.

Anion Recognition in Aqueous Media by Cyclopeptides and Other Synthetic Receptors.

Anion receptors often rely on coordinative or multiple ionic interactions to be active in water. In the absence of such strong interactions, anion binding in water can also be efficient, however, as demonstrated by a number of anion receptors developed in recent years. The cyclopeptide-derived receptors comprising an alternating sequence of l-proline and 6-aminopicolinic acid subunits are an example. These cyclopeptides are neutral and, at first sight, can only engage in hydrogen-bond formation with an anionic substrate. Nevertheless, they even interact with strongly solvated sulfate anions in water. The intrinsic anion affinity of these cyclopeptides can be related to structural aspects of their highly preorganized concave binding site, which comprises a wall of hydrophobic proline units arranged around the peptide NH groups at the cavity base. When anions are incorporated into this cavity they can engage in hydrogen-bonding interactions to the NH groups, and complex formation also benefits from cavity dehydration. Formation of 1:1 complexes, in which an anion binds to a single cyclopeptide ring, is associated with only small stability constants, however, whereas significantly more stable complexes are formed if the anion is buried between two cyclopeptide molecules. A major contribution to the formation of these sandwich complexes derives from the addition of the second ring to the initially formed 1:1 cyclopeptide-anion complex. This step brings the apolar proline residues of both cyclopeptides in close proximity, which causes the resulting structure to be stabilized to a large extent by hydrophobic effects. Solvent dependent binding studies provided an estimate to which degree these solvent effects contribute to the overall complex stability. In these studies, bis(cyclopeptides) were used, featuring two cyclopeptide rings covalently connected via linkers that enable both rings to simultaneously interact with the anion. Bis(cyclopeptides) with additional solubilizing groups allowed binding studies in a wide range of solvents, including in water. The systematic analysis of the solvent dependence of anion affinity yielded a quantitative correlation between complex stability and parameters relating to the solvation of the anions and solvent properties, confirming that solvent effects contribute to anion binding. Interestingly, the thermodynamic signature of complex formation in water mirrors that of sulfate binding to a protein complex but is opposite to that of other recently described anion receptors, which also do not engage in ionic or coordinative interactions with the substrate. These receptors not only differ in terms of the thermodynamics of binding from the cyclopeptides but also possess a characteristically different anion selectivity in that they prefer to bind weakly coordinating anions but fail to bind sulfate. Solvent effects likely control the anion binding of both receptors types but their impact on complex formation and anion selectivity seems to be profoundly different. Future work in the area of anion coordination chemistry will benefit from the deeper understanding of these effects and how they can be controlled.

Human norovirus GII.4(MI001) P dimer binds fucosylated and sialylated carbohydrates.

Human noroviruses (HuNoV), members of the family Caliciviridae, are the major cause of acute viral gastroenteritis worldwide. Successful infection is linked to the ability of the protruding (P) domain of the viral capsid to bind histo-blood group antigens (HBGA). Binding to gangliosides plays a major role for many nonhuman calici- and noroviruses. Increasing evidence points to a broader role of sialylated carbohydrates such as gangliosides in norovirus infection. Here, we compare HBGA and ganglioside binding of a GII.4 HuNoV variant (MI001), previously shown to be infectious in a HuNoV mouse model. Saturation transfer difference nuclear magnetic resonance spectroscopy, native mass spectrometry (MS) and surface plasmon resonance spectroscopy were used to characterize binding epitopes, affinities, stoichiometry and dynamics, focusing on 3'-sialyllactose, the GM3 ganglioside saccharide and B antigen. Binding was observed for 3'-sialyllactose and various HBGAs following a multistep binding process. Intrinsic affinities (Kd) of fucose, 3'-sialyllactose and B antigen were determined for the individual binding steps. Stronger affinities were observed for B antigen over 3'-sialyllactose and fucose, which bound in the mM range. Binding stoichiometry was analyzed by native MS showing the presence of four B antigens or two 3'-sialyllactose in the complex. Epitope mapping of 3'-sialyllactose revealed direct interaction of α2,3-linked sialic acid with the P domain. The ability of HuNoV to engage multiple carbohydrates emphasizes the multivalent nature of norovirus glycan-specificity. Our findings reveal direct binding of a GII.4 HuNoV P dimer to α2,3-linked sialic acid and support a broader role of ganglioside binding in norovirus infection.

High-Throughput Agonist Shift Assay Development for the Analysis of M1-Positive Allosteric Modulators

Agonist shift assays feature cross-titrations of allosteric modulators and orthosteric ligands. Information generated in agonist shift assays can include a modulator’s effect on the orthosteric agonist’s potency (alpha) and efficacy (beta), as well as direct agonist activity of the allosteric ligand (tauB) and the intrinsic binding affinity of the modulator to the unoccupied receptor (KB). Because of the heavy resource demand and complex data handling, these allosteric parameters are determined infrequently during the course of a drug discovery program and on a relatively small subset of compounds. Automation of agonist shift assays enables this data-rich analysis to evaluate a larger number of compounds, offering the potential to differentiate compound classes earlier and prospectively prioritize based on desired molecular pharmacology. A high-throughput calcium-imaging agonist shift assay was pursued to determine the allosteric parameters of over 1000 positive allosteric modulator (PAM) molecules for the human muscarinic acetylcholine receptor 1 (M1). Control compounds were run repeatedly to demonstrate internal consistency. Comparisons between potency measurements and the allosteric parameter results demonstrate that these different types of measurements do not necessarily correlate, highlighting the importance of fully characterizing and understanding the allosteric properties of leads.

From optimized monovalent ligands to size-controlled dendrimers: an efficient strategy towards high-activity DC-SIGN antagonists

This short review describes our work on the development of dendrimeric antagonists of DC-SIGN, a dendritic cells (DCs) receptor recognizing highly mannosylated structures and primarily involved in the recognition of viruses such as HIV. The structure of pseudo-di-mannoside and pseudo-tri-mannoside compounds was first finely modified to obtain DC-SIGN ligands that were more stable and selective than mannose. Their DC-SIGN affinity differences were amplified once presented on multivalent dendrimer-like scaffolds, including poly-alkyne terminated and phenylene-ethynylene rod-like ones. Libraries of mannosylated dendrimers were synthesized, improving their stability and maximizing their monodispersity. The effect of the dendrimers valency, structure, and size on DC-SIGN affinity and antiviral potency was investigated. Both the valency and the topology of the architectures were revealed as key parameters for activity optimization, together with the intrinsic affinity of the monovalent ligand. The stability, rigidity, and length of the scaffolds were also tuned. The design of geometrically adapted scaffolds afforded one of the most potent inhibitors of DC-SIGN mediated HIV infections to date. This monodispersed, not cytotoxic, and highly active compound was also tested with DCs; its internalization into endolysosomal compartments and its ability to induce the overexpression of signaling molecules makes it a good precursor to produce pathogen-entry inhibitors with immunomodulant properties.

Investigating the Influence of Membrane Composition on Protein-Glycolipid Binding Using Nanodiscs and Proxy Ligand Electrospray Ionization Mass Spectrometry.

This work describes a versatile analytical approach, which combines the proxy ligand electrospray ionization mass spectrometry (ESI-MS) assay and model membranes of defined composition, to quantify the influence of lipid bilayer composition on protein-glycolipid binding in vitro. To illustrate the implementation of the assay (experimental design and data analysis), affinities of the monosialoganglioside ligand GM1, incorporated into nanodiscs (NDs), for cholera toxin B subunit homopentamer (CTB5) were measured. A series of NDs containing GM1 and cholesterol were prepared using three different phospholipids (1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)), and the average GM1 and cholesterol content of each ND were determined. The intrinsic affinities of GM1-containing NDs prepared with the three phospholipids are found to be similar in magnitude, indicating that small differences in the fatty acid chain length and the number of unsaturated bonds do not significantly affect the CTB5-GM1 interaction. Moreover, the measured affinities are similar to the value measured for GM1 pentasaccharide, indicating that neither the ceramide moiety nor the surface of the phospholipid membrane plays a significant role in CTB5 binding. The intrinsic (per binding site) affinity of the CTB5-GM1 interaction was found to decrease with increasing GM1 content of the ND, consistent with the occurrence of GM1 clustering in the membrane, which sterically hinders binding to CTB5. Notably, the addition of cholesterol to GM1-containing NDs did not have a significant effect on the strength of the CTB5-GM1 interaction. This result, which is at odds with the findings of a previous study of CTB5 binding to GM1 in vesicles, suggests that cholesterol does not "mask" GM1, at least not in NDs. These data, in addition to providing new insights into the influence of membrane composition on CTB5-GM1 binding, demonstrate the potential of the proxy ligand ESI-MS approach for comprehensive and quantitative studies of lectin interactions with glycolipids in native-like, membrane environments.