O-phthalaldehyde based quantification of polysaccharide modification in conjugate vaccines.

Polysaccharide-based vaccines cannot stimulate long-lasting immune response in infants due to their inability to elicit a T-cell-dependent immune response. This has been addressed using conjugation technology, where conjugates were produced by coupling a carrier protein to polysaccharides using different conjugation chemistries, such as cyanylation, reductive amination, ethylene diamine reaction, and others. Many glycoconjugate vaccines that are manufactured using different conjugation technologies are already in the market for neonates, infants and young children (e.g., Haemophilus influenzae type-b, Streptococcus pneumoniae and Neisseria meningitidis vaccines), and all of them elicit a T-cell dependent immune response. To manufacture glycoconjugate vaccines, the capsular polysaccharide is first activated by converting its hydroxyl groups to aldehyde-, cyanyl-, or cyanate ester groups, depending on the conjugation chemistry selected. The oxidized and reduced aldehyde functional groups of the polysaccharides are subsequently reacted with the amino groups of carrier protein by reductive amination to form a stable amide bond. In CDAP-based conjugation, the polysaccharide -OH groups are activated to form cyanyl-, or cyanate ester groups to react with the amino groups of carrier protein and forms an isourea bond. Understanding the extent of polysaccharide activation/modification is essential since it directly influences the molar mass of the conjugate, its stability, and the immunogenicity of the product. Reported methods are available to estimate the aldehyde groups of polysaccharides generated by reductive amination. However, no method is available to quantify the cyanyl or cyanate ester (-OCN) groups generated by cyanylation with 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP). We report a novel strategy using an O-phthalaldehyde (OPA) derivatization process followed by size-exclusion chromatography (SEC) high-performance liquid chromatography (HPLC) separation and UV detection. The cyanate ester groups on the activated polysaccharide directly reveal the extent of polysaccharide activation/modification and the residual activated groups in the purified conjugates. This method would be useful for conjugate vaccine manufacturing using CDAP chemistry.

Individual polysaccharide quantification in polyvalent pneumococcal conjugate vaccine using rate nephelometry.

The multivalent pneumococcal conjugate vaccine (PCV) contains purified polysaccharides of different serotypes conjugated to a carrier protein. Testing the final formulated product for individual serotype polysaccharide content is critical in vaccine quality control which requires an assay specific to each serotype polysaccharide present in the formulated product. Antibodies specific to the serotypes specific polysaccharide were used in rate nephelometry assay for quantifying individual serotype polysaccharides in the formulated vaccine. Generally, native polysaccharide (NP) have been used as reference standard. However, the polysaccharide antigen in the vaccine product is in the conjugate form (CRM197 linked) and hence using NP as a reference standard may not be suitable. Activated quenched polysaccharide (AQP) as a reference standard in rate nephelometry would be more appropriate. The epitope structure of AQP closely represents the polysaccharide-protein conjugate drug product (DP) after trypsin digestion. Hence, AQP was evaluated as a novel reference standard for the accurate and precise determination of individual polysaccharides in the multivalent DP. Rate nephelometry assay using AQP could be used for DP release and stability for monitoring time-dependent changes in the product and establishing the shelf life. A similar strategy could be applied to test and release monovalent or multivalent polysaccharide-protein conjugate vaccines (Meningococcal, Haemophilus influenza Type B, Typhoidal, and non-typhoidal salmonella).

High-Performance Anion-Exchange chromatography with conductivity detection method for simultaneous determination of nitrogen and phosphorus in polysaccharides.

Capsular polysaccharides of Streptococcus pneumoniae contain a characteristic mix of monosaccharides in their structure resulting in immunologically distinct serotypes. Pneumococcal capsular polysaccharides include sugars such as hexoses, uronic acids, hexosamines, methyl pentoses, other functional groups are attached to the sugars are N and O-acetyl groups, nitrogen and phosphorus. Most of these components can be quantified using different colorimetric methods. However, available methods for quantifying nitrogen and phosphorus are not sensitive enough and laborious. We report a highly sensitive high-performance anion-exchange chromatography-conductivity detector (HPAEC-CD) method for quantifying nitrogen and phosphorus present in pneumococcal capsular polysaccharides. The method is reliable, robust and reproducible with no interference. The LOQ for nitrogen and phosphorus of 3.125 and 62.5 ng/mL, respectively, is highly critical for estimating low levels of total nitrogen and total phosphorus. We have implemented this method to quantify total nitrogen in Typhoid Vi polysaccharide and phosphorus in Haemophilus influenzae type-b polysaccharide. This method has greater application for quantification of nitrogen and phosphorus present in low concentrations in polysaccharide vaccines/biologicals.

A reversed phase HPLC-UV method for the simultaneous determination of residual formaldehyde and Triton X-100 in vaccine products.

Many of the inactivated viral vaccines for human and animal use are manufactured using formaldehyde as an inactivating agent. Apart from formaldehyde, Triton X-100 is also one of the chemicals commonly used in viral vaccine manufacturing. Triton X-100 is typically used to extract the cell-associated viruses and / or components during manufacturing process. The concentration of formaldehyde and Triton X-100 in the final bulks are also reduced during vaccine purification process. Here we report a simple RP-HPLC-UV based method for the quantification of residual Triton X-100 and formaldehyde as process impurities in viral vaccines. This method is also adopted for the residual impurity determination of either formaldehyde or Triton X-100 in other non-viral vaccines, multivalent as well as sub-unit vaccines, such as liquid pentavalent, includes TT, DT, Hepatitis B (rDNA) and Haemophilus type b conjugate vaccine (adsorbed). This method is rapid and can quantify both Triton X-100 and formaldehyde in a single preparation with improved peak asymmetry. This new assay has a linearity range starting from 0.0625 to 1 µg/mL for formaldehyde and 0.625-10 µg/mL for Triton X-100. This method would be very useful for viral vaccine manufacturing and release.

2-Phenoxyethanol: A novel reagent for improved sensitivity of carbohydrate quantification.

Anthrone is a routinely used reagent for estimating carbohydrates (Polysaccharides) in research, development and pharmaceutical applications. In presence of sulphuric acid, the polysaccharide gets hydrolyzed to monosaccharides in the form of hydroxymethyl furfural or furfural. The furfural then reacts with anthrone to form a green color complex with a maximum absorbance at 625 nm. Though anthrone reacts well with polysaccharides containing hexoses (such as glucose and galactose) and rhamnose, it is less reactive with uronic acids (such as glucuronic acid and galacturonic acid) and hexosamines (such as fucosamine, glucosamine, galactosamine, mannosamine, pneumosamine). Here, we report a novel reagent, 2-Phenoxyethanol, which reacts with furfural or hydroxymethyl furfural resulting in higher absorptivity. This method is rapid, sensitive, simple and direct, and can be used for quantitative determination of any type of carbohydrate that contains neutral sugars and uronic acids. For these saccharides, the sensitivity of the assay using 2-Phenoxyethanol (2-PE) is twice over anthrone method. Uronic acids show improved sensitivity using 2-PE over Phenol and it is more than twice with glucuronic acid. 2-PE reagent method has greater application for quantification of carbohydrates when present in low concentration in vaccines/biologicals.

E6 protein of human papillomavirus 16 (HPV16) expressed in Escherichia coli sans a stretch of hydrophobic amino acids, enables purification of GST-ΔE6 in the soluble form and retains the binding ability to p53.

Recombinant E6 expressed in Escherichia coli is known to form recalcitrant inclusion bodies even when fused to the soluble GST protein. This study describes the modification of the HPV genotype-16 oncogenic protein E6 in order to obtain it in the soluble form. The modified protein (ΔE6) was expressed in E. coli BL21 as an N-terminal fusion with GST (GST-ΔE6). ΔE6 was constructed by deleting the nucleotide sequences coding for IHDIIL (31-36 a.a), one of the highly hydrophobic peptide stretches, using splicing by overextension polymerase chain reaction (SOE-PCR). The removal of IHDIIL residues rendered the GST-ΔE6 soluble and amenable for purification involving a two step process a preliminary glutathione-GST affinity chromatography followed by gel-filtration chromatography. Evaluation of purified protein fractions by HPLC suggests that GST-ΔE6 exists as a monomer. Further, the ΔE6 in GST-ΔE6 seemed to retain the binding ability to p53 as determined by the glutathione-GST capture ELISA. Purified GST-ΔE6 we reckon, might find use as an essential reagent in immunological assays, in sero-epidemiological studies, and also in studies to delineate the structure and function of HPV16 E6.

A simple and rapid method to monitor the disassembly and reassembly of virus-like particles.

Protein fluorescence spectra (~300-440 nm) could be used as a simple and sensitive method to monitor the disassembly and reassembly of virus-like particles (VLPs). Insect cell expressed and purified HPV-16 L1 VLPs show significantly high fluorescence intensity, whereas the fluorescence is almost quenched after disassembly by adding the reducing agent. By removing the reducing agent, the fluorescence was restored to its original intensity, indicating the reassembly of VLPs. The data are consistent with enzyme-linked immunosorbent assay (ELISA) reactivity using conformation-specific mouse monoclonal antibody. The same method could be extended to VLPs of other viruses.

Activity of E. coli ClpA bound by nucleoside diphosphates and triphosphates.

The Escherichia coli ClpA protein is a molecular chaperone that binds and translocates protein substrates into the proteolytic cavity of the tetradecameric serine protease ClpP. In the absence of ClpP, ClpA can remodel protein complexes. In order for ClpA to bind protein substrates targeted for removal or remodeling, ClpA requires nucleoside triphosphate binding to first assemble into a hexamer. Here we report the assembly properties of ClpA in the presence of the nucleoside diphosphates and triphosphates ADP, adenosine 5'-[γ-thio]triphosphate, adenosine 5'-(ß,γ-imido)triphosphate, ß,γ-methyleneadenosine 5'-triphosphate, and adenosine diphosphate beryllium fluoride. In addition to examining the assembly of ClpA in the presence of various nucleotides and nucleotide analogues, we have also correlated the assembly state of ClpA in the presence of these nucleotides with both polypeptide binding activity and enzymatic activity, specifically ClpA-catalyzed polypeptide translocation. Here we show that all of the selected nucleotides, including ADP, promote the assembly of ClpA. However, only adenosine 5'-[γ-thio]triphosphate and adenosine 5'-(ß,γ-imido)triphosphate promote the formation of an oligomer of ClpA that is active in polypeptide binding and translocation. These results suggest that the presence of γ phosphate may serve to switch ClpA into a conformational state with high peptide binding activity, whereas affinity is severely attenuated when ADP is bound.

Application of the sequential n-step kinetic mechanism to polypeptide translocases.

Clp/Hsp100 proteins are essential motor proteins in protein quality control pathways in all organisms. Such enzymes couple the energy derived from ATP binding and hydrolysis to translocate and unfold polypeptide substrates. Often they perform this role in collaboration with proteases for protein removal or with other chaperones for protein disaggregation. Unlike other well-characterized motor proteins, fundamental parameters such as the microscopic rate constants and overall rate of translocation, step-size (amino acids translocated per step), processivity, and directionality are not available for many of these enzymes. We have recently developed a fluorescence stopped-flow method to elucidate these fundamental mechanistic details. In addition, we have developed a quantitative method to examine the single-turnover time courses that result from the rapid mixing experiments. With these two advances in hand, we have recently reported the first determination of the microscopic rate constants, overall rate of translocation, kinetic step-size, and processivity for the E. coli ClpA polypeptide translocase. Here, we report a description of both the fluorescence stopped-flow method to examine the mechanism of enzyme catalyzed polypeptide translocation and the mathematics required to quantitatively examine the resulting time courses.

Effect of substituents of alloxazine derivatives on the selectivity and affinity for adenine in AP-site-containing DNA duplexes.

Using the DNA duplex containing an AP site (5'-TCC AGX GCA AC-3'/3'-AGG TCN CGT TG-5', X = AP site, N = A, T, C, or G), we have found that 2-amino-4-hydroxypteridine (pterin) selectively binds to guanine (G), and that the enhanced binding affinity for G is obtained by its methylated derivative 2-amino-6,7-dimethyl-4-hydroxypteridine (diMe pteridine). Similarly, among the cytosine (C)-selective ligands, i.e. derivatives of 2-amino-1,8-naphthyridine, a trimethyl-substituted derivative (2-amino-5,6,7-trimethyl-1,8-naphthyridine) selectively binds to C with a strong binding affinity of 1.9 × 10(7) M(-1). In the case of lumazine derivatives, pteridine-2,4(1H,3H)-dione (lumazine) binds to adenine (A), and its methylated derivative, 6,7-dimethylpteridine-2,4(1H,3H)-dione (diMe lumazine) strongly binds to A with enhanced binding affinity, keeping the same base-selectivity. On the other hand, the benzo-annelated (with phenyl ring, 2.4 Å) derivative of lumazine, benzo[g]pteridine-2,4(1H,3H)-dione (alloxazine), can bind to A selectively, whereas its methylated ligand, 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione (lumichrome) selectively binds to thymine (T) over A, C and G. Methyl-substituted lumichrome derivatives show moderate binding affinities for target nucleobases. The changes in the base-selectivity and binding affinities are discussed in detail with respect to the substituents of these ligands, considering hydrogen-bonding patterns, size of AP site and stacking interactions.

Molecular mechanism of polypeptide translocation catalyzed by the Escherichia coli ClpA protein translocase.

The removal of damaged or unneeded proteins by ATP-dependent proteases is crucial for cell survival in all organisms. Integral components of ATP-dependent proteases are motor proteins that unfold stably folded proteins that have been targeted for removal. These protein unfoldases/polypeptide translocases use ATP to unfold the target proteins and translocate them into a proteolytic component. Despite the central role of these motor proteins in cell homeostasis, a number of important questions regarding the molecular mechanisms of enzyme catalyzed protein unfolding and translocation remain unanswered. Here, we demonstrate that Escherichia coli ClpA, in the absence of the proteolytic component ClpP, processively and directionally steps along the polypeptide backbone with a kinetic step size of approximately 14 amino acids, independent of the concentration of ATP with a rate of approximately 19 amino acids s(-1) at saturating concentrations of ATP. In contrast to earlier studies by others, we have developed single-turnover fluorescence stopped-flow methods that allow us to quantitatively examine the molecular mechanism of the motor component ClpA decoupled from the proteolytic component ClpP. For the first time, we reveal that in the absence of ClpP ClpA translocates polypeptides directionally, processively and in discrete steps similar to other motor proteins that translocate vectorially on a linear lattice, such as nucleic acid helicases and kinesin. We believe that the methods employed here will be generally applicable to the examination of other AAA+ protein translocases involved in a variety of important biological functions where the substrate is not covalently modified; for example, membrane fusion, membrane transport, protein disaggregation, and protein refolding.

Effect of the bases flanking an abasic site on the recognition of nucleobase by amiloride.

BACKGROUND: We explain here the various non-covalent interactions which are responsible for the different binding modes of a small ligand with DNA. METHODS: The combination of experimental and theoretical methods was used. RESULTS: The interaction of amiloride with thymine was found to depend on the bases flanking the AP site and different binding modes were observed for different flanking bases. Molecular modeling, absorption studies and binding constant measurements support for the different binding patterns. The flanking base dependent recognition of AP site phosphates was investigated by (31)P NMR experiments. The thermodynamics of the ligand-nucleotide interaction was demonstrated by isothermal titration calorimetry. The emission behavior of amiloride was found to depend on the bases flanking the AP site. Amiloride photophysics in the context of AP-site containing DNA is investigated by time-dependent density functional theory. CONCLUSIONS: Flanking bases affect the ground and excited electronic states of amiloride when binding to AP site, which causes flanking base-dependent fluorescence signaling. GENERAL SIGNIFICANCE: The various noncovalent interactions have been well characterized for the determination of nucleic acid structure and dynamics, and protein-DNA interactions. However, these are not clear for the DNA-small molecule interactions and we believe that our studies will bring a new insight into such phenomena.

Small-molecule binding at an abasic site of DNA: strong binding of lumiflavin for improved recognition of thymine-related single nucleotide polymorphisms.

The binding behavior of lumiflavin, a biologically vital ligand, with DNA duplexes containing an abasic (AP) site and various target nucleobases opposite the AP site is studied. Lumiflavin binds selectively to thymine (T) opposite the AP site in a DNA duplex over other nucleobases. Using 1H NMR spectroscopy and fluorescence measurements, we show that ligand-DNA complexation takes place by hydrogen-bond formation between the ligand and the target nucleobases and by stacking interactions between the ligand and the nucleobases flanking the AP site. From isothermal titration calorimetric experiments, we find that ligand incorporation into the AP sites is primarily enthalpy-driven. Examination of ionic strength dependency of ligand binding with DNA reveals that ligand-DNA complexation is a manifestation of both electrostatic and nonelectrostatic interactions and that the contribution from the nonelectrolyte effect is fundamental for the stabilization of the ligand-DNA complex. In comparison to riboflavin, reported previously as a T-selective ligand, lumiflavin binds to the DNA much more strongly and is a more promising ligand for efficient detection of T-related single nucleotide polymorphisms.

Simultaneous recognition of nucleobase and sites of DNA damage: effect of tethered cation on the binding affinity.

BACKGROUND: The 3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide (DCPC-NH(2)) has been synthesized and characterized by Mass and (1)H NMR. The selective binding of the ligand to thymine (T) target base is investigated by the melting temperature (T(m)) and fluorescence measurements. METHODS: Thermal denaturation study of DNA duplex containing T target base revealed the DeltaT(m) of 5.1 degrees C, while least influence was observed for other target bases. The fluorescence of the ligand DCPC-NH(2) is quenched only upon adding the DNA containing T target base. RESULTS: The binding constant for the interaction of the ligand to T target base containing DNA duplex was determined to be 4.7 (+/-0.3)x10(6) M(-1). The tethered cation in the ligand is found to enhance the binding constant. The ligand binds to both a target nucleotide and an AP site on the complimentary strand for the target strand in a DNA duplex. GENERAL SIGNIFICANCE: Interestingly, the electronic behavior of the ligand depends on the bases flanking the AP site. Its fluorescence is quenched with guanine flanking bases, while it is enhanced with DNA duplex containing T bases flanking an AP site. Finally, the binding modes were visualized by molecular modeling.

Effect of methyl substitution in a ligand on the selectivity and binding affinity for a nucleobase: a case study with isoxanthopterin and its derivatives.

Isoxanthopterin (IX) has two edges with hydrogen bond-forming sites suitable for binding to thymine (T) and cytosine (C). The binding affinity of IX for T or C is stronger than for adenine (A) and guanine (G), whereas the base selectivity of IX for T over C (and vice versa) is moderate. In order to improve both the binding affinity and base selectivity for T over C or C over T, a methyl group is introduced respectively at the N-3 or N-8 position of IX. This leads to the known ligands 3-methyl isoxanthopterin (3-MIX) and 8-methyl isoxanthopterin (8-MIX), and the binding affinity for C or T is expected to be tuned and improved by methyl substitution. Indeed, 3-MIX selectively binds to T more strongly than IX with a binding constant of 1.5 x 10(6) M(-1) and it loses its binding affinity for C. In contrast, 8-MIX selectively binds to C over T with a binding constant of 1.0 x 10(6) M(-1) and the binding affinity is greatly improved compared to the parent ligand IX. The thermodynamics of the ligand-nucleotide interaction is analyzed by isothermal calorimetric titrations, and the results show that the interaction follows a 1:1 stoichiometry and is enthalpy-driven. The introduction of methyl groups at both N-3 and N-8 positions results in an increase in enthalpy of the ligand-nucleotide interaction, which leads to the improved binding affinity.

6,7-Dimethyllumazine as a potential ligand for selective recognition of adenine opposite an abasic site in DNA duplexes.

6,7-Dimethyllumazine more selectively binds to adenine (A) base opposite the abasic site in DNA duplexes (5'-TCC AGX[combining low line] GCA AC-3'/3'-AGG TCN CGT TG-5', X = AP site (Spacer C3), N= A, T, C and G) than the other three nucleobases with a dissociation constant K(d) of ca. 1.0 microM; substituted methyl groups enhance the binding affinity to A and the selectivity for A over T, compared to the parent molecule, lumazine.

Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms.

Alloxazine can bind to adenine selectively over other nucleobases opposite an abasic site in DNA duplexes (5'-TCC AGX GCA AC-3'/3'-AGG TCN CGT TG-5', X=AP site, N=A, T, C, G) with a dissociation constant of 0.82 microM (pH 7.0, I=0.11 M, at 5 degrees C), and it is applicable to SNPs typing of PCR amplification products based on the binding-induced fluorescence response.

Improvement of base selectivity and binding affinity by controlling hydrogen bonding motifs between nucleobases and isoxanthopterin: application to the detection of T/C mutation.

At an abasic site in an oligo-DNA duplex, isoxanthopterin (IX)(dagger) can bind to thymine (T) and cytosine (C) with strong affinity compared to adenine and guanine, but the base selectivity for T against C is moderate. In order to improve both binding affinity and base selectivity for T against C, a methyl group is introduced to IX, which is known as 3-methyl isoxanthopterin (3-MIX),(dagger) by which binding affinity for C is expected to decrease. Indeed, 3-MIX specifically binds to T more strongly than IX and loses its binding affinity for C. The improved binding ability of 3-MIX for T would be suitable for the practical use in SNP typing related to T.