Supplementary Information. Profiling Formulated Monoclonal Antibodies by 1 H NMR Spectroscopy

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1 Supplementary Information Profiling Formulated Monoclonal Antibodies by 1 H NMR Spectroscopy Leszek Poppe 1 *, John B. Jordan 1, Ken Lawson 2, Matthew Jerums 2, Izydor Apostol 2 and Paul D. Schnier 1 1 Molecular Structure and Characterization, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California Process and Product Development, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California A B Figure 1S. 1D 1 H NMR spectra of a formulated antibody recorded with A) 1D NOESY presat and B) PGSTE at 52 C. In both cases an identical number of scans and receiver gain were used. Note that spectrum A is scaled by the factor of ¼.

2 Figure 2S. Temperature variation of 1 H PGSTE NMR spectra for a typical IgG1 molecule. Spectra on the left are of increasing temperature (bottom to top) and spectra on the right are of decreasing temperature (top to bottom). Note that the intensities of the water, polysorbate and sugar resonances decrease while the overall intensity of the protein increases with temperature.

3 Figure 3S. Flowchart of the PROFILE and H-PROFILE data processing. The operations in the upper and lower boxes are performed with Topspin 3.0 (Bruker-Biospin) and Matlab (MathWorks, Inc.), respectively. Functions in bold correspond to the software syntax.

4 Figure 4S. Demonstration of the PROFILE subtraction algorithm. Two samples of IgG1 were measured, with 0.1% (S1) and without polysorbate 80 (PS-80) (S2) A) Spectrum of S1 overlaid with the spectrum of 0.1% PS-80 in the same buffer (gray). B) PROFILE spectra of sample S1 after buffer subtraction C) PROFILE spectra of sample S2. The correlation obtained from the PROFILE spectra: r p (PROFILE(S1-buffer),PROFILE(S2))=0.992, which is within the limits of experimental reproducibility.

5 Figure 5S. Influence of the signal to noise ratio on the cross correlation coefficient of PROFILE spectra. The PROFILE contour spectrum is modeled as a box function with the unit intensity and the PROFILE fingerprint spectrum as a modulated sine function with the intensity of 0.2 (inset). Various levels (λ) of random noise were added to both signals and the correlation coefficient r was calculated as a product: r(box+λ*noise 1,box+λ*noise 2 )* r(sine+λ*noise 1,sine+ λ*noise 2 ), where noise 1 and noise 2 are two uncorrelated noise vectors with RMSD values of 1, and the fraction of signal range is 0.8. The S/N = λ -1.

6 Figure 6S. Influence of the signal to noise ratio on the cross correlation coefficient of 2D 15 N- 1 H TROSY spectra. The spectrum is represented by ~40 Hz wide Gaussian peak shape which closely approximates peak shapes from traces of the 2D spectra. Various levels (λ) of random noise were added and the correlation coefficient, r, was calculated as a product: peak+λ*noise 1,peak+λ*noise 2, where noise 1 and noise 2 are two uncorrelated noise vectors with RMSD values of 1, and the fraction of signal range is The S/N = λ -1. The inset represents S/N=45, corresponding to the correlation coefficient of 0.99.

7 Figure 7S. The PGSTE pulse sequence used in the PROFILE experiments. The filled large and small polygons are the diffusion and the spoiler gradient respectively, with smoothed rectangular shape. φ 1 =x,-x; φ 2 =x,x,y,y,-x,-x,-y,-y, φ 3 =8x,8y,8(-x),9(-y), φ 4 =32x, 32y, 32(-x), 32(-y); φ 5 =2(x,- x,-y,y,-x,x,y,-y,-x, x, y,-y,x,-x,-y,y), 2(-x,x,y,-y,x,-x,-y,y,x,-x,-y,y,-x,x,y,-y) Figure 8S. H-PROFILE for an IgG1 sample recorded at at two different temperatures The red (r) and the black (b) spectra were used to calculate R 2, R 1 and D t ratio from eqs. S2-S6. The displayed spectra were recorded with the following sets of parameters: R 2 : g(r,b)=56.5 G/cm, δ(r,b)=1 ms τ b =50 µs, τ r =350 µs (b)=100 ms, (r)=99.55 ms; R 1 : g(b)=56.6 G/cm, g(r)=40 G/cm δ(r,b)=1 ms, (b)=100 ms, (r)=200 ms; D t : g(b)=42.4 G/cm, g(r)=28.3 G/cm, δ(r,b)=2 ms, (r,b)=100 ms. Standard errors were obtained from three experiments with different sets of pulse program parameters.

8 Determination of the relaxation rates and diffusion coefficients from PGSTE experiment In the PGSTE experiment shown in Figure 7S the signal intensity can be factored in the following way 1 : S = S 0 e 4(δ+τ)R 2 e γ H 2 σ 2 g 2 δ 2 D t +σ δ+ 3τ 2 e R 1Δ (S1) where R 2 is the transverse relaxation rate, D t is the translational diffusion coefficient and R 1 is the longitudinal relaxation rate. The experimental parameters: γ H, g, δ, σ, σ τ and correspond to the proton gyromagnetic ratio, gradient strength, gradient duration, gradient shape factors, short delay, and diffusion delay, respectively. The relaxation rates R 1 or R 2 from two PGSTE experiments are recorded with (Δ 1, g 1 ) and (Δ 2, Δ 1 Δ 2 g 1 ) or (τ 1, 1 ) and τ 2, 1 3(τ 2 τ 1 ) 2 parameter sets respectively. If the ratios of the corresponding signal intensities are λ1 for the R 1 experiment and λ2 for the R 2 expriment, one can easily show that the relaxation rates can be calculated from the following relationships: R 1 = ln(λ1) Δ 2 Δ 1 R 2 = ln(λ2) 4(τ 2 τ 1 ) (S2) (S3) The relative translational diffusion coefficients can be obtained from the PGSTE experiments recorded with two different gradients strengths g1 and g2 for each protein sample: S 1 (g 1 ), S 2 (g 2 ) and S 1 (g 1 ), S 2 (g 2 ) which can be combined to give: ε = ln S 1 S 2 ε = ln S 1 S 2 D t D t = ε ε = β (S4) (S5) (S6) Using the Stokes-Einstein relationships: R 2 ~η R H 3 and D t ~η 1 R H 1, where η is the viscosity and R H is the hydrodynamic radius, one can obtain the following two hydrodynamic ratios:

9 R H R H = (α β) 1 2 (S7) η η = α 1 2 β 3 2 Where α = R 2 is the ratio of transverse relaxation rates and β = D t is the ratio of translational R 2 D t diffusion coefficients. When the relative measurements correspond to different temperatures, T* and T, α and β should be replaced with α T and β T T T in the above equations. A Monte Carlo simulation showed that to a good approximation, up to n% random error of the signal intensity propagates into n% standard error for the hydrodynamic radii or viscosity ratios. The standard error for the ratios of the hydrodynamic parameters was also estimated from the different H- PROFILE experiments (different combinations of g 1,g 2,τ 1,τ 2 parameters) and was less than 2%. (S8) References (1) Sinnaeve, D. Concepts in Magn. Reson. 2012, 40A(2),