Strategies for the production of isotopically labelled Fab fragments of therapeutic antibodies in Komagataella phaffii (Pichia pastoris) and Escherichia coli for NMR studies.

The importance and fast growth of therapeutic monoclonal antibodies, both innovator and biosimilar products, have triggered the need for the development of characterization methods at high resolution such as nuclear magnetic resonance (NMR) spectroscopy. However, the full power of NMR spectroscopy cannot be unleashed without labelling the mAb of interest with NMR-active isotopes. Here, we present strategies using either Komagataella phaffii (Pichia pastoris) or Escherichia coli that can be widely applied for the production of the antigen-binding fragment (Fab) of therapeutic antibodies of immunoglobulin G1 kappa isotype. The E. coli approach consists of expressing Fab fragments as a single polypeptide chain with a cleavable linker between the heavy and light chain in inclusion bodies, while K. phaffii secretes a properly folded fragment in the culture media. After optimization, the protocol yielded 10-45 mg of single chain adalimumab-Fab, trastuzumab-Fab, rituximab-Fab, and NISTmAb-Fab per liter of culture. Comparison of the 2D-1H-15N-HSQC spectra of each Fab fragment, without their polyhistidine tag and linker, with the corresponding Fab from the innovator product showed that all four fragments have folded into the correct conformation. Production of 2H-13C-15N-adalimumab-scFab and 2H-13C-15N-trastuzumab-scFab (>98% enrichment for all three isotopes) yielded NMR samples where all amide deuterons have completely exchanged back to proton during the refolding procedure.

Backbone and side-chain resonance assignments of the NISTmAb-scFv and antigen-binding study.

Monoclonal antibodies (mAbs) therapeutics are the largest and fastest growing class of biologic drugs, amongst which, the vast majority are immunoglobulin G1 (IgG1). Their antigen binding abilities are used for the treatment of immunologic diseases, cancer therapy, reversal of drug effects, and targeting viruses and bacteria. The high importance of therapeutic mAbs and their derivatives has called for the generation of well-characterized standards for method development and calibration. One such standard, the NISTmAb RM 8621 based on the antibody motavizumab, has been developed by the National Institute of Standards and Technologies (NIST) in the US. Here, we present the resonance assignment of the single chain variable fragment, NISTmAb-scFv, that was engineered by linking the variable domains of the heavy and light chains of the NISTmAb. Also, addition of a peptide, corresponding to the target antigen of motavizumab, to samples of NISTmAb-scFv has induced chemical shift perturbations on residues lining the antigen binding interface thereby indicating proper folding of the NISTmAb-scFv.

Assessment of the higher order structure of Humira®, Remicade®, Avastin®, Rituxan®, Herceptin®, and Enbrel® by 2D-NMR fingerprinting.

The advent of monoclonal antibody biosimilar products has stimulated the development of analytical methods that can better characterize an important quality attribute, namely the higher order structure (HOS). Here, we propose a simple approach based on heteronuclear 2D NMR techniques at natural abundance for generating spectral fingerprints of the HOS at high resolution. We show that the proposed method can assess the HOS of six therapeutic products, adalimumab (Humira®), bevacizumab (Avastin®), infliximab (Remicade®), rituximab (Rituxan®), trastuzumab (Herceptin®), and Etanercept (Enbrel®). After treatment with immobilized papain, the purified fragments (Fab and Fc) were analyzed by 2D proton-nitrogen and proton-carbon NMR correlations. All Fab and Fc fragments produced high-resolution 2D-NMR spectra from which assessment of their higher order structure can be performed in the context of comparability studies. In particular, the two different sequences of Fc fragments could be unambiguously distinguished. The results show that it is possible to obtain structurally dependent information at amino acid resolution of these important therapeutic agents.

Application of 2D-NMR with room temperature NMR probes for the assessment of the higher order structure of filgrastim.

The higher order structure (HOS) of biotherapeutics is a critical quality attribute that can be evaluated by nuclear magnetic resonance (NMR) spectroscopy at atomic resolution. NMR spectral mapping of HOS can be used to establish HOS consistency of a biologic across manufacturing changes or to compare a biosimilar to an innovator reference product. A previous inter-laboratory study performed using filgrastim drug products demonstrated that two-dimensional (2D)-NMR 1HN-15NH heteronuclear correlation spectroscopy is a highly robust and precise method for mapping the HOS of biologic drugs at natural abundance using high sensitivity NMR 'cold probes.' Here, the applicability of the 2D-NMR method to fingerprint the HOS of filgrastim products is demonstrated using lower sensitivity, room temperature NMR probes. Combined chemical shift deviation and principal component analysis are used to illustrate the performance and inter-laboratory precision of the 2D-NMR method when implemented on room temperature probes.

Assessment of the structure of pegylated-recombinant protein therapeutics by the NMR fingerprint assay.

A number of recombinant protein therapeutic products, such as filgrastim (methionyl granulocyte colony stimulating factor [Met-GCSF] used to boost the immune system in chemotherapy treated cancer patients), and interferon alpha-2 (used for the treatment of various viral infections), have been chemically modified with the addition of a polyethylene glycol (PEG) chain. This modification prolongs residency of the drug in the body and reduces metabolic degradation, which allows less frequent administration of the products. Here we show how NMR spectroscopy methods can assess the higher order structure (HOS) of pegylated-filgrastim (Neulasta®), pegylated interferon-α2a (Pegasys®) pegylated interferon-α2b (PEG-Intron®) purchased from the marketplace. The addition of the PEG moiety effectively doubles the molecular weight of the three products. This presents a significant challenge for the application of NMR techniques. Nevertheless, the results showed that high-resolution spectra could be recorded for two of the three products. Comparison of the spectra of the pegylated protein and the non-pegylated protein shows that the chemical modification did not alter the HOS of these proteins.

Monitoring Effects of Excipients, Formulation Parameters and Mutations on the High Order Structure of Filgrastim by NMR.

PURPOSE: Filgrastim is the generic name for recombinant methionyl human granulocyte colony-stimulating factor (r-metHuG-CSF). It is marketed under the brand name Neupogen® by Amgen. Since this product has lost patent protection, many biosimilar versions have been approved or are in the process of filing for market authorization throughout the world. Here we show that NMR spectroscopy can be used to assess the three-dimensional structure of the active ingredient in the formulated approved product Neupogen®. METHODS: Recombinant metHuG-CSF was prepared in E. coli and isotopically enriched with (13)C and (15) N isotopes. NMR spectroscopy was used to study the effects of excipients on the conformation. RESULTS: The effects of pH variation on the amide chemical shifts suggest the presence of cation-pi interactions between His-79 and Trp-118, and His-156-Trp-58-His-52 that stabilizes the conformation at low pH. This may be associated with a small local conformational change. The NMR data showed that polysorbate does not interact significantly with filgrastim thus allowing the collection of spectra in the presence of 20 times the formulation concentration in the sample. However, at higher detergent concentrations a reduction of signal intensity is observed. Conclusions The NMR fingerprint assay applied to filgrastim (Neupogen® and a CRS from the European Pharmacopeia (EP)) provided residue specific information of the structure of the drug substance. In addition to current methods, the ability to assess the conformation with a high degree of resolution can greatly facilitate comparability exercises.

A single N-acetylgalactosamine residue at threonine 106 modifies the dynamics and structure of interferon α2a around the glycosylation site.

Enzymatic addition of GalNAc to isotopically labeled IFNα2a produced in Escherichia coli yielded the O-linked glycoprotein GalNAcα-[(13)C,(15)N]IFNα2a. The three-dimensional structure of GalNAcα-IFNα2a has been determined in solution by NMR spectroscopy at high resolution. Proton-nitrogen heteronuclear Overhauser enhancement measurements revealed that the addition of a single monosaccharide unit at Thr-106 significantly slowed motions of the glycosylation loop on the nanosecond time scale. Subsequent addition of a Gal unit produced Gal(ß1,3)GalNAcα-[(13)C,(15)N]IFNα2a. This extension resulted in a further decrease in the dynamics of this loop. The methodology used here allowed the first such description of the structure and dynamics of an O-glycoprotein and opens the way to the study of this class of proteins.

Stereochemistry of 10-sulfoxidation catalyzed by a soluble Delta9 desaturase.

The stereochemistry of castor stearoyl-ACP Delta(9) desaturase-mediated 10-sulfoxidation has been determined. This was accomplished by (19)F NMR analysis of a fluorine-tagged product, 18-fluoro-10-thiastearoyl ACP S-oxide, in combination with a chiral solvating agent, (R)-AMA. Sulfoxidation proceeds with the same stereoselectivity as hydrogen removal from the parent stearoyl substrate. These data validate the use of thia probes to determine the stereochemistry and cryptoregiochemistry of desaturase-mediated oxidations.

Assessment of the effects of pH, formulation and deformulation on the conformation of interferon alpha-2 by NMR.

This article reports the results of our investigation of the effects of pH and various formulations on the conformation of interferon (IFN) alpha-2a and IFN alpha-2b using the NMR fingerprinting assay. Samples of (15)N-IFN alpha-2 were produced and their activity was inferred by comparing their NMR spectra with those recorded for the corresponding European Directorate for the Quality of Medicines (EDQM) reference standards. The proteins were then mixed with appropriate excipients to reproduce formulations used in innovator products of Roferon-A and Intron-A and deformulated via cation-exchange chromatography. The conformation of IFN alpha-2 was monitored by two-dimensional (2D)-NMR spectroscopy at various pHs, after formulation and deformulation procedures. Our results show that the process does not alter the conformation of IFN alpha-2 and that the optimal pH for deformulation is 4.0 +/- 0.5. Variation in pH below 3.0 causes the protein to unfold, whereas above pH 4.5, the three-dimensional (3D) fold is maintained, but the NMR spectra indicate a propensity to oligomerize. This behaviour is reversible upon readjusting the pH to 3.5-4.5. Here, we demonstrate the applicability of NMR to assess the structure of protein therapeutics. The proposed method can assist in validating analytical methods that require deformulation of IFN-based products.

Synthesis of chiral fluorine-tagged reference standards for the (19)F NMR-based stereochemical analysis of sulfoxides at trace analytical levels.

Chiral fluorine-tagged sulfoxides of known absolute configuration have been synthesized. These compounds are required as reference standards to validate a (19)F NMR-based micromethod for the stereochemical analysis of biosynthetic fatty acyl sulfoxides.

NMR assignment of the N-terminal TRAF-like RING zinc finger domain of human FLN29.

Resistance of cancer cells to oncotherapeutics designed to trigger programmed cell death (a.k.a. apoptosis) greatly limits clinical efficacy. The human FLN29 protein may play a role in this process via protein-protein interactions. Here we report the NMR spectral assignment of the N-terminal TRAF2/6-RING-zinc finger-like domain of this protein.

In vitro enzymatic oxidation of a fluorine-tagged sulfido substrate analogue: a 19F NMR investigation.

1H-decoupled 19F NMR has been used to monitor the highly regioselective oxidation of a fluorine-tagged thia-fatty acid derivative by castor stearoyl-ACP delta9 desaturase. The major enzymatic product, after reductive work-up, was identified as 9-fluoro-1-nonanol. This compound could be easily distinguished from substrate and a 9-sulfoxy by-product on the basis of its 19F NMR chemical shift and spiking experiments using authentic standards. Structural assignment of the cleavage product was confirmed by GC-MS analysis of the enzymatic products.

Quantitation of hydroxylated byproduct formation in a Saccharomyces cerevisiae Delta9 desaturating system.

The distribution of products obtained from stearoyl CoA Delta9 desaturase-mediated oxidation in Saccharomyces cerevisiae has been measured directly for the first time using an omega-fluorinated fatty acid substrate.

Concerning the origin of 19F-19F NMR COSY and NOESY connections in the spectra of perfluorooctanoic acid, R(F)-palmitic acid-F13 and diethyl perfluorosuberate.

A combination of 19F nuclear Overhauser effects (NOE) and molecular mechanics calculations are presented for delineating the spatial origin of the well-known four-bond 19F-19F COSY connections which are generally observed in the 19F NMR spectra of compounds containing perfluorinated chains. Perfluorooctanoic acid (PFOA), R(F)-palmitic acid-F13 and diethyl perfluorosuberate were used as test cases. Spin-lattice relaxation times (T1) are included and NOESY correlations through three and four bonds occur.

A micromethod for the stereochemical analysis of fatty acid desaturase-mediated sulfoxidation reactions.

The stereochemistry of fatty acid desaturase-mediated sulfoxidation can be evaluated at micromolar concentrations of analyte using (19)F NMR in combination with a chiral shift reagent: (S)-(+)-MPAA.

Iridium luminophore complexes for unimolecular oxygen sensors.

In this study, a series of novel luminescent cyclometalated Ir(III) complexes has been synthesized and evaluated for use in unimolecular oxygen-sensing materials. The complexes Ir(C6)(2)(vacac), 1, Ir(ppy)(2)(vacac), 2, fac-Ir(ppy)(2)(vppy), 3, and mer-Ir(ppy)(2)(vppy), 4, where C6 = Coumarin 6, vacac = allylacetoacetate, ppy = 2-phenylpyridine, and vppy = 2-(4-vinylphenyl)pyridine, all have pendent vinyl or allyl groups for polymer attachment via the hydrosilation reaction. These luminophore complexes were characterized by NMR, absorption, and emission spectroscopy, luminescence lifetime and quantum yield measurements, elemental analysis, and cyclic voltammetry. Complex 1 was structurally characterized using X-ray crystallography, and a series of 1-D ((1)H, (13)C) and 2-D ((1)H-(1)H, (1)H-(13)C) NMR experiments were used to resolve the solution structure of 4. Complexes 1 and 3 displayed the longest luminescence lifetimes and largest quantum efficiencies in solution (tau = 6.0 micros, phi = 0.22 for 1; tau = 0.4 micros, phi = 0.2 for 3) and, as result, are the most promising candidates for future luminescence-quenching-based oxygen-sensing studies.

Synthesis and Structural Investigations of [Mn(3)O(4)(phen)(4)(H(2)O)(2)](NO(3))(4).2.5H(2)O: A Water-Bound Complex Obtained by Cerium(IV) Oxidation.

The trinuclear manganese complex [Mn(3)O(4)(phen)(4)(H(2)O)(2)](NO(3))(4).2.5H(2)O, 1 (where, phen = 1,10-phenanthroline), has been synthesized by the Ce(IV) oxidation of a concentrated solution of manganese(II) acetate and phen in 1.6 N nitric acid. The complex crystallizes in the triclinic space group P&onemacr; with a = 10.700(2) Å, b = 12.643(3) Å, c = 20.509(4) Å, alpha = 78.37(3) degrees, beta = 83.12(3) degrees, gamma = 82.50(3) degrees, and Z = 2. The structure was solved by direct methods and refined by least-squares techniques to the conventional R (R(w)) factors of 0.055 (0.076) based on 4609 unique reflections with F(o) >/= 6.0sigma(F(o)). The structure of the cation consists of an oxo-bridged Mn(3)O(4)(4+) core, with the geometry of the manganese atoms being octahedral. The coordination polyhedron of one of the manganese atoms (Mn(1)) consists of two &mgr; oxo ligands and two pairs of nitrogen atoms of two phen moieties, whereas that of each of the remaining two manganese atoms consists of three &mgr;-oxo ligands, two nitrogen atoms of a phen moiety, and the oxygen atom of a water molecule. The complex represents the second example for water coordination to manganese(IV) centers in complexes with a Mn(3)O(4)(4+) core. Optical spectra in ligand buffer (pH 4.5) reveal complete conversion of the complex into a Mn(III)Mn(IV) species. The observed room-temperature (298 K) magnetic moment of 3.75 &mgr;(B) indicates the presence of strong antiferromagnetic coupling in the complex.