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Introduction: PF-06439535 (bevacizumab-bvzr; Zirabev®) is a bevacizumab biosimilar. The stability profile and functional activity of PF-06439535 after dilution for intravenous infusion was evaluated following extended storage conditions. Methods: PF-06439535 drug product was diluted in 0.9% sodium chloride to produce final concentrations of 1.4 and 16.5 mg/mL of PF-06439535, representing clinically relevant low and high doses for intravenous infusion. Three drug product lots and three infusion bag types (polyolefin, ethylene vinyl acetate, and polyvinyl chloride) were tested. To simulate the potential preparation and administration conditions encountered in a clinical setting, prepared drug solutions were initially stored at 25 ± 5°C for 24 ± 2 h, and then at 5 ± 3°C for up to 6 weeks. Extended storage was followed by storage at 25 ± 5°C for 24 ± 2 h before testing. Physicochemical and biological stability were evaluated according to visual characteristics and pH, protein concentration, particulate content, the proportions of molecular weight variants and charge variants, and relative potency. A wide range of analytical techniques optimized for PF-06439535 assessment were employed, such as size-exclusion chromatography, non-reducing sodium dodecyl sulfate capillary electrophoresis, cation-exchange chromatography, far-UV circular dichroism spectroscopy, differential scanning calorimetry, and an in vitro cell-based bioassay. Results: For all concentrations, drug product lots, infusion bag types, and time points tested, there were no significant changes in protein concentration and no notable differences in visual characteristics (color, clarity, and visible particulates). The abundance of molecular weight variants and charge variants remained stable over the 6-week study period. There were no stability concerns with regard to sub-visible particles. There were no significant changes in primary, secondary, or tertiary structure. Finally, the in vitro relative potency of PF-06439535 was maintained throughout the study period. Conclusions: The stability and biological activity of PF-06439535 was maintained after dilution and storage for up to 6 weeks at 2–8°C, demonstrating the integrity of diluted PF-06439535 under extended in-use conditions. [ABSTRACT FROM AUTHOR]

Introduction: The stability and functional activity of the trastuzumab biosimilar PF-05280014 (trastuzumab-qyyp; TrazimeraTM), was assessed under extended in-use conditions. Methods: PF-05280014 was diluted in 0.9% sodium chloride to final concentrations of 0.2 mg/mL and 4 mg/mL in 3 different types of infusion bags (polyolefin, ethylene vinyl acetate, and polyvinyl chloride). Infusion bags containing diluted PF-05280014 were stored at 25 ± 5° C for 24 h, before storage at 5 ± 3° C for 0, 1, 2, 4, or 6 weeks. Following extended storage, samples of PF-05280014 were removed from the infusion bags and stored at 25 ± 5° C for 24 h before biophysical and functional characterization. In addition to the visual characteristics of each sample at the various time points, the stability of PF-05280014 was assessed using a variety of biophysical techniques, including size-exclusion high-performance liquid chromatography, non-reducing sodium dodecyl sulfate capillary electrophoresis, cation-exchange chromatography, peptide mapping, far-UV circular dichroism spectroscopy, and differential scanning calorimetry. The functional activity of PF-05280014 was evaluated using a cell-based growth inhibition assay. Results: For all PF-05280014 concentrations, time points and infusion bags tested, there were no significant differences in visual characteristics or in protein concentration. The were no significant changes in the relative abundance of molecular weight or charge variants throughout the 6-week study period. Similarly, there were no significant changes in primary structure or in secondary structure content during the study. The relative potency of PF-05280014 was also maintained throughout the 6-week period. Conclusions: The stability and functional activity of PF-05280014 was maintained following dilution in 0.9% sodium chloride and storage for up to 6 weeks at 2–8° C. [ABSTRACT FROM AUTHOR]

RAMPED-UP NMR method is presented which generates simple spectra, which are easy to interpret, and allows several proteins to be screened simultaneously. The ability of three different proteins to be analyzed simultaneously for binding to two different ligands is demonstrated.

The drug discovery process relies on characterizing structure-activity relationships, since specific ligand-target interactions often result in important biological functions. Measuring diffusion coefficients by nuclear magnetic resonance spectroscopy is a useful way to study binding, because changes can be detected when a small ligand interacts with a macromolecular target. Diffusion coefficients can be miscalculated, however, due to magnetization transfer between the receptor and ligand. This transferred nuclear Overhauser effect (trNOE) disrupts the observed signal decay due to diffusion as a function of the experimental diffusion time. Since longer diffusion times also selectively edit free ligand signal, the measured diffusion coefficients become biased toward the fraction of bound ligand. Despite this discrepancy, under these experimental conditions, the trNOE selectively influences the measured signals of binding ligands and can be used to gain insight into ligand-protein interactions. These phenomena have been studied for caffeine and L-tryptophan, which bind to human serum albumin, and the antimalarial agent trimethoprim, which interacts with dihydrofolate reductase. The results provide insight into the nature of ligand-protein binding and are thus useful for elucidating the molecular features of the ligand that interact with the protein.

Results reveal that the hydrogen bond network contributed by the first 15 amino acid residues of aporubredoxin or their interaction with other parts of the protein confer thermostability to the bacterial apo- and holoaporubredoxins.

A complete relative stereochemistry of an organic molecule with five stereocenters is determined by the use of Residual Dipolar Couplings (RDCs) in combination with molecular order matrix calculations. The stereochdmical assignments of the stereocenters obtained by using only RDC is in perfect agreement with the X-ray crystallographic study.

Research has been conducted on six-membered chairlike rings. The method developed for determination of the relative structure elements in these rings is described.

Diffusion-based NMR techniques are widely used in the pharmaceutical industry for a variety of methods like screening of chemical mixtures or determining the structures of bound ligands without physical separation. Diffusion deviation is a good method for characterization of the ligand isotope and to build epitope map diffusion, data was collected with a long diffusion time.

Residual dipolar couplings (RDCs), induced by aligned cosolutes, have revolutionized biomolecular three-dimensional structures prediction, which has led to the development of different methods of predicting alignment tensors making RDCs easier to interpret. Studies are conducted to create a different approach to derive an expression for the alignment tensor induced by a neutral as well as a dilute cosolute.

Abstract: We have discovered a novel bacterial polysaccharide structural element, 3-O-acetylglycerol, in the Streptococcus pneumoniae ST11A polysaccharide: Display Omitted This moiety was elucidated through a combination of homonuclear and heteronuclear 1D and 2D NMR experiments using 1H, 13C, and 31P in various combinations. The 3-O-acetylglycerol moiety is substoichiometrically O-acetylated in ST11A; yet, key connectivities that unequivocally show O-acetylation at the glycerol are provided by the long-range correlations from the acetate methyl groups to the glycerol in the 1H–13C HMBC spectrum. Additionally, we clarify the 1H–31P assignments previously presented. [Copyright &y& Elsevier]

The human gamma-herpesviruses Epstein–Barr virus (EBV) (HHV-4) and Kaposi's sarcoma-associated herpesvirus (KSHV) (HHV-8) are responsible for a number of diseases, including various types of cancer. Epstein–Barr nuclear antigen 1 (EBNA1) from EBV and latency-associated nuclear antigen (LANA) from KSHV are viral-encoded DNA-binding proteins that are essential for the replication and maintenance of their respective viral genomes during latent, oncogenic infection. As such, EBNA1 and LANA are attractive targets for the development of small-molecule inhibitors. To this end, we performed a biophysical screen of EBNA1 and LANA using a fragment library by saturation transfer difference (STD)–NMR spectroscopy and surface plasmon resonance (SPR). We identified and validated a number of unique fragment hits that bind to EBNA1 or LANA. We also determined the high-resolution crystal structure of one fragment bound to EBNA1. Results from this screening cascade provide new chemical starting points for the further development of potent inhibitors for this class of viral proteins. [ABSTRACT FROM AUTHOR]

EBNA1 inhibitors developed by fragment-based drug design block EBNA1 DNA binding and EBV-dependent tumor cell growth in vivo. No holds Barr-ed for cancer treatment: Persistent latent infection with Epstein-Barr virus contributes to tumorigenesis in a variety of cancer types. The only viral protein that is consistently expressed in these tumors is Epstein-Barr nuclear antigen 1, which performs a variety of biological functions. To target this antigen, Messick et al. designed a series of chemical inhibitors and then tested them in vitro and in multiple mouse models of Epstein-Barr virus–associated cancer. The authors characterized the inhibitors using a variety of assays, examined the mechanism by which they work, and demonstrated preclinical effectiveness and suitable pharmacological properties, paving the way for further therapeutic development. Epstein-Barr virus (EBV) is a DNA tumor virus responsible for 1 to 2% of human cancers including subtypes of Burkitt's lymphoma, Hodgkin's lymphoma, gastric carcinoma, and nasopharyngeal carcinoma (NPC). Persistent latent infection drives EBV-associated tumorigenesis. Epstein-Barr nuclear antigen 1 (EBNA1) is the only viral protein consistently expressed in all EBV-associated tumors and is therefore an attractive target for therapeutic intervention. It is a multifunctional DNA binding protein critical for viral replication, genome maintenance, viral gene expression, and host cell survival. Using a fragment-based approach and x-ray crystallography, we identify a 2,3-disubstituted benzoic acid series that selectively inhibits the DNA binding activity of EBNA1. We characterize these inhibitors biochemically and in cell-based assays, including chromatin immunoprecipitation and DNA replication assays. In addition, we demonstrate the potency of EBNA1 inhibitors to suppress tumor growth in several EBV-dependent xenograft models, including patient-derived xenografts for NPC. These inhibitors selectively block EBV gene transcription and alter the cellular transforming growth factor–β (TGF-β) signaling pathway in NPC tumor xenografts. These EBNA1-specific inhibitors show favorable pharmacological properties and have the potential to be further developed for the treatment of EBV-associated malignancies. [ABSTRACT FROM AUTHOR]

A correction to the article "The structure of the capsular polysaccharide of pneumococcal serotype 11A reveals a novel acetylglycerol that is the structural basis for 11A subtypes" that was published in the 2011 issue is presented.

Despite the emerging impact of serogroup 11 serotypes in Streptococcus pneumoniae epidemiology, the structures of serogroup 11 capsule types have not been fully elucidated, particularly the locations of O-acetyl substitutions. Here, we report the complete structures of the serotype 11B, 11C, and 11F polysaccharides and a revision to the serotype 11A capsular polysaccharide using nuclear magnetic resonance (NMR). All structures shared a linear, tetrasaccharide backbone with a pendant phosphopolyalcohol. Three of four saccharides are conserved in all serotypes. The individual serotype capsules differed in the identity of one saccharide, the pendant phosphopolyalcohol, and the O-acetylation pattern. Though the assigned locations of O-acetate substitutions in this study differed from those of previous reports, our findings were corroborated with strong correlations to serology and genetics. We examined the binding of serotyping sera to serogroup 11 polysaccharides by using flow cytometry and an inhibition-type enzyme-linked immunosorbent assay (ELISA) and found that de-O-acetylation of capsular polysaccharides by mild hydrolysis decreases its immunoreactivity, supporting the crucial role of O-acetylation in the antigenicity of these polysaccharides. Due to strong correlations between polysaccharide structures and capsule biosynthesis genes, we were able to assign target substrates for the O-acetyltransferases encoded by wcwC, wcwR, wcwT, and wcjE. We identified antigenic determinants for serogroup 11 serotyping sera and highlight the idea that conventional serotyping methods are not capable of recognizing all putative variants of S. pneumoniae serogroup 11. [ABSTRACT FROM AUTHOR]

Streptococcus pneumoniae (pneumococcus) expresses a capsular polysaccharide (CPS) that protects against host immunity and is synthesized by enzymes in the capsular polysaccharide synthesis (cps) locus. Serogroup 11 has six members (11A to -E) and the CPS structure of all members has been solved, except for serotype 11D. The cps loci of 11A and 11D differ by one codon (N112S) in wcrL, which putatively encodes a glycosyl transferase that adds the fourth sugar of the CPS repeating unit (RU). Gas chromatography and nuclear magnetic resonance analysis revealed that 11A and 11D PSs contain identical CPS RUs that contain αGlc as the fourth sugar. However, ~25% of 11D CPS RUs contain instead αGlcNAc as the fourth sugar, suggesting that 11D wcrL encodes a bispecific glycosyltransferase. To test the hypothesis that codon 112 of WcrL determines enzyme specificity, and therefore the fourth sugar in the RU, we generated three isogenic pneumococcal strains with 11A cps loci containing wcrL encoding Ser-112 (MBO128) or Ala-112 (MBO130). MBO128 was serologically and biochemically identical to serotype 11D. MBO130 has a unique serologic profile; has as much αGlcNAc as 11F, 11B, and 11C CPS do; and may represent a new serotype. These findings demonstrate how pneumococci alter their CPS structure and their immunologic properties with a minimal genetic change. [ABSTRACT FROM AUTHOR]

A correction to the article "Elucidation of Structural and Antigenic Properties of Pneumococcal Serotype 11A, 11B, 11C and 11F Polysaccharide Capsules" that was published in a 2011 issue is presented.

Residual dipolar couplings (RDCs), in combination with molecular order matrix calculations, were used to unambiguously determine the complete relative stereochemistry of an organic compound with five stereocenters. Three simple one-dimensional experiments were utilized for the measurements of 13C-¹H, 13C-19F, 19F-¹H, and ¹H-¹HRDCs. The order matrix calculation was performed on each chiral isomer independently. The fits were evaluated by the comparison of the root-mean-square deviation RDC of calculated and measured RDCs. The order tensor simulations based on two different sets of RDC data collected with phage and bicelles are consistent. The resulting stereochemical assignments of the stereocenters obtained from using only RDCs are in perfect agreement with those obtained from the single- crystal X-ray structure. Six RDCs are found to be necessary to run the simulation, and seven are the minimum to get an acceptable result for the investigated compound. It was also shown that 13C-¹H and ¹H-¹H RDCs, which are the easiest to measure, are also the most important and information-rich data for the order matrix calculation. The effect of each RDC on the calculation depends on the location of the corresponding vector in the structure. The direct RDC of a stereocenter is important to the configuration determination, but the configuration of stereocenters devoid of protons can also be obtained from analysis of nearby RDCs. [ABSTRACT FROM AUTHOR]

Reports on diffusion-based nuclear magnetic resonance (NMR) techniques that have been incorporated into a variety of methods such as screening of chemical mixtures. Monitoring of the diffusion coefficient that enables the ligand-receptor interaction by the direct observation of the ligand signals; Characterization of the ligand epitope by the diffusion deviation.

Fragonomics is the process of using small, relatively simple molecules to generate chemical starting points for hit generation. Fragonomics has come of age and is now one of the major concepts in hit generation. What is its future?

Fragment screening by saturation transfer difference nuclear magnetic resonance (STD-NMR) is a robust method for identifying small molecule binders and is well suited to a broad set of biological targets. STD-NMR is exquisitely sensitive for detecting weakly binding compounds (a common characteristic of fragments), which is a crucial step in finding promising compounds for a fragment-based drug discovery campaign. This protocol describes the development of a library suitable for STD-NMR fragment screening, as well as preparation of protein samples, optimization of experimental conditions, and procedures for data collection and analysis.

We have undertaken a structural assessment of Streptococcus pneumoniae 11A polysaccharide as well as two clinical isolates related to 11A. The clinical isolates were labeled 11Aalpha and 11Abeta. The result of our experiments is a revision to the old structure for S. pneumoniae 11A polysaccharide. The new structure differs from the old structure in both the primary connectivities and acetylation pattern. We also show that 11A contains an acetylglycerol-PO4 moiety, a substitution that is heretofore unknown in the bacterial polysaccharide literature. The two clinical isolates were also structurally characterized. 11Aalpha was determined to be identical to 11A. 11Abeta is a new serotype, which differs from 11A in the absence of the acetylation of the glycerol-PO4 moiety and a different acetylation pattern of the saccharides. Thus, we propose that the acetylglycerol is the structural basis for 11Aalpha and 11Abeta subtypes.

Fragment-based drug discovery (FBDD) needs a biophysical assay to complement, or even replace, biochemical screening. NMR is the best choice for this because NMR delivers many different types of data that impacts medicinal chemistry decisions. There are a multitude of different NMR methods which can be employed to these ends. The choice of which method to use will be different for every need. We discuss the different methods, the data they produce, and how they are best utilized in a FBDD setting.

Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for the structure determination of biomolecules through NMR spectroscopy. Recent advances have proven it to be a valuable tool for determination of the stereochemistry of organic molecules. By simple inspection or order matrix calculations, RDCs provide unambiguous information about the relative configurations or complete stereochemistry of organic compounds., (Copyright 2004 John Wiley & Sons, Ltd.)

A novel methodology using the order matrix calculation to determine the absolute sign of spin-spin couplings based on the structure of organic compounds is presented. The sign of the residual dipolar coupling (RDC) depends on the sign of corresponding scalar spin-spin coupling constant and the sign of the RDC has a dramatic influence on the order matrix calculation. Therefore, the sign of the spin-spin coupling constant can be obtained by an order matrix calculation through the corresponding RDC. Six types of spin-spin coupling constants, including 2J(H,H), 1J(C,F), 2J(C,F), 3J(C,F), 2J(F,H) and 3J(F,H), were obtained simultaneously. Except for 3J(C,F) where the measured RDCs have very small magnitudes, the signs were determined unambiguously., (Copyright 2004 John Wiley & Sons, Ltd.)

The drug discovery process often involves the screening of compound libraries to identify drug candidates capable of binding to target macromolecules. New approaches in biological and chemical research are driving a change in the pharmaceutical industry. Recent advances in NMR spectroscopy such as affinity NMR techniques, which detect binding of a small molecule with a "receptor", have been shown to be valuable tools to perform rapid screening of compounds for biological activity. These NMR observable events include using relaxation, chemical shift perturbations, translational diffusion, and magnetization transfer. These one dimensional NMR methods increase both the throughput of screening and yield crucial data on the mode of binding. The practical utility of these techniques will be described.