CN114878621A - Method for quantitatively evaluating structure of protein drug based on high-field nuclear magnetic resonance technology - Google Patents
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Abstract
The invention discloses a method for quantitatively evaluating a protein drug structure based on a high-field nuclear magnetic resonance technology, relates to the field of protein drug research and development and product quality control, and particularly relates to a method for quantitatively evaluating a protein drug covalent structure and a high-level spatial structure based on the high-field nuclear magnetic resonance technology. The method uses unmarked test samples and standard samples to collect 2D nuclear magnetic resonance experiments, and comprehensively, accurately and conveniently quantitatively evaluates the structure of the protein drugs. Firstly, the method uses a TOCSY spectrum and a NOESY spectrum to simultaneously evaluate the similarity of the covalent structure and the spatial structure of the protein drug, and the evaluation of the structure is more comprehensive; secondly, the method comprehensively considers the chemical shift and the relative intensity change of all signals for quantitative analysis, so that the analysis structure is more accurate; finally, the method does not need to use professional computing software to carry out a large amount of time-consuming calculation analysis, is simple and easy to implement, and is very suitable for popularization and application.
Description
Technical Field
The invention relates to the field of research and development of protein drugs and product quality control, in particular to a method for quantitatively evaluating a covalent structure and a high-level spatial structure of a protein drug based on a high-field nuclear magnetic resonance technology.
Background
Biological agents that have been approved to date have been used for the treatment of cancer, viral infections, immunodeficiency and other diseases, where proteinaceous drugs such as recombinant proteins, biological enzymes, monoclonal or polyclonal antibodies account for a very large proportion (Steven K et al, N Engl J Med,2011,365(5): 385-. Under the new crown epidemic situation, in the research of specific drugs aiming at new crown virus at home and abroad, the protein drugs are either a neutralizing antibody aiming at S protein or ACE2 protein or an analog of ACE2 protein. The structure of a protein molecule includes not only covalent structures but also higher-order structures such as the spatial folding condition, conformational uniformity, dynamic properties of the protein, and aggregation state between molecules. The structure of a protein molecule is important for the efficacy and safety of its pharmaceutical effect (Wang D, et al, Molecules,2021,26(14): 4251). The molecular structure of the protein is easily affected by the environment, such as the pH value and ionic strength of a buffer system, and meanwhile, the protein expression and purification process is complicated, and the molecules are easily modified, oxidized and the like, so that the overall structure of the protein is affected. Therefore, the establishment of a set of accurate and convenient quantitative assessment method for the protein structure has important significance for the research and development of bionic protein medicines and the quality control of the medicines at the later stage after the medicines are on the market.
With the improvement of the field intensity of modern nuclear magnetic resonance and the use of a low-temperature probe, the resolution and the sensitivity of the nuclear magnetic resonance are greatly improved. Besides conventional small molecule structure identification, liquid nuclear magnetic resonance technology has been widely used in the research of biomacromolecules including proteins and nucleic acids as a molecular structure identification means with high accuracy and no damage to samples. There are some works in the literature for quantitative assessment of the advanced structure of drugs using nuclear magnetic resonance, and the comparison system is a series of works published by the drug evaluation and research center of the U.S. food and drug administration from 2016 (Ghasriani H et al, Nat Biotechnol,2016,34(2): 139-41; Chen K, et al, AAPS PharmSciTech,2018,19(3): 1011-. In the work, 1D hydrogen spectra and 2D heteronuclear spectra of protein samples obtained by the same protein sample in different laboratories and different instruments and different ways are analyzed, and the analysis method comprises direct chemical shift comparison and PCA analysis and then the Mahalanobis distance is calculated. The results show that chemical shift differences of less than 0.008ppm and mahalanobis distances of less than 3.3 can be considered to be the same molecule. It is known that the chemical shift and intensity of the NOESY spectrum signal of nuclear magnetic resonance can more truly reflect the space structure of protein molecule, 1DThe information given by hydrogen spectra and 2D heteronuclear spectra is limited, and the article also indicates that PCA analysis of 2D spectra requires a large number of calculations depending on mathematical software, which is extremely time-consuming and data-intensive. It is therefore more difficult to perform PCA analysis using the more informative NOESY spectra. Assessment of protein structure using NOESY profile comparison in 2007 in a group of seville
et al, J Chem Inf Model,47(3):737-43), the analytical methods used in the article, the first method did not take into account signal intensity, the second and third methods did not take into account all signals, nor did all methods give a clear evaluation criterion. And the protein is easily modified during the expression process to influence the drug effect, and the covalent structure of covalent modification cannot be evaluated by using NOESY spectrum only.
Disclosure of Invention
The invention aims to provide a method for simply, accurately and comprehensively quantitatively evaluating the structure of a protein drug based on a high-field nuclear magnetic resonance technology, which uses low-cost and unmarked samples and standard substances to collect a 2D nuclear magnetic resonance experiment and adopts a simple and comprehensive analysis method to accurately quantitatively evaluate the structure of the protein drug including a covalent structure and a high-grade structure.
Aiming at the above purpose, the invention is realized by the following technical scheme:
a method for quantitatively evaluating the structure of protein drugs based on a high-field nuclear magnetic resonance technology comprises the following steps:
high-field nuclear magnetic resonance 2D for collecting protein drug standard sample and test sample 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 H NOESY spectrum, which is used for processing the spectrogram data and improving the quality and resolution of the spectrogram;
comparing 2D of standard and test samples 1 H- 1 H TOCSY spectrum, marking the signal with difference in chemical shift in fingerprint area, reading the chemical shift, calculating the root mean square value of the two-dimensional chemical shift difference, and calculating the two-dimensional chemical shift differenceThe difference root mean square value is used for evaluating the similarity of the covalent structures of the protein drug standard sample and the test sample;
comparing 2D of standard and test samples 1 H- 1 The H NOESY spectrum is characterized in that signals with changed chemical shift and intensity in NH-NH, NH-CH and CH-CH regions of the spectrum are marked, the chemical shift and the relative intensity of the signals are read, the root mean square value of two-dimensional chemical shift difference is calculated, the spatial distance difference of two samples based on the relative intensity of the signals is calculated, and the similarity of the spatial structures of the protein drug standard sample and the test sample is evaluated together according to the root mean square value and the spatial distance difference of the two-dimensional chemical shift difference.
Further, the following treatments were performed on the protein drug standard sample and the test sample in advance: dissolving a sample in a buffer system without hydrogen with the pH value less than 7.5, adding inorganic salt according to the actual condition of the sample to stabilize the spatial structure of the sample, and adding 10% of heavy water for field locking shimming.
Further, a PBS buffer system is selected as the buffer system without hydrogen element.
Further, the concentration of the protein sample is greater than 0.1 mM.
Further, the step of processing the spectrogram comprises: solvent pressing, addition of a window function, fourier transform, baseline phase calibration and linear prediction.
Further, 2D 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 H NOESY spectra were collected using different NMR instruments with ultra low temperature probes above 500MHz depending on the actual molecular weight of the sample.
Further, 2D 1 H- 1 The mixing time of the H TOCSY spectrum is set to be 80 ms; 2D 1 H- 1 The mixing time of the H NOESY spectrum is between 50 and 200ms, determined in particular by the molecular weight of the protein, which decreases for higher molecular weights and vice versa.
Further, the NOE signal is selected as the signal with the changed intensity, spectrograms with different mixing time can be collected for comparison during experimental collection, and the NOE signal with strong signal and no signal which is obviously more than that of the experiment with short mixing time is selected as the best NOE signal.
Further, the root mean square value of the two-dimensional chemical shift difference is calculated by
Wherein delta x And delta y The difference in chemical shift in the x and y dimensions, respectively.
Further, the relative signal intensity is equal to the ratio of the label signal intensity to the reference signal dispersed in the spectrogram, and the reference signal of the spectrograms of the two samples is the same signal in the two spectrograms.
Further, the spatial distance difference of the two samples refers to the relative distance difference of the test sample relative to the standard sample, the NOE signal intensity is inversely proportional to the sixth power of the spatial distance, and the calculation formula is
I Sign board And I Measuring The relative intensities of the signals of the standard sample and the test sample, respectively.
Further, 2D 1 H- 1 The fingerprint area of the H TOCSY spectrogram refers to a related signal area of amino hydrogen of a protein main chain and all hydrogen in residues, and the chemical shift range is (6-9 ppm, -2-6 ppm).
Further, 2D 1 H- 1 The chemical shift ranges of NH-NH, NH-CH and CH-CH regions of the H NOESY spectrum are (6-9 ppm ), (6-9 ppm, -2-6 ppm) and (-2-6 ppm ) regions with signals respectively.
Further, the condition that the covalent structure and the spatial structure of the protein drug are consistent is that: the two-dimensional chemical shift difference has a root mean square value of less than 0.008ppm and a spatial range difference of less than + -10% for all intensity signals, wherein the spatial range difference of the intensity signals is less than + -5% and most of them is less than + -2%.
The method comprises the steps of firstly, using a high-field nuclear magnetic resonance instrument (not less than 500MHz, specifically according to the conditions of the molecular weight of a sample and the like) with an ultralow-temperature probe to collect 2D (two-dimensional) of a standard sample and a test sample 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 H NOESY spectrum, and quantitatively comparing chemical shift and relative intensity of spectrum signals, thereby evaluating the difference of covalent structure and space structure of the protein.
Compared with the prior art, the invention has the following beneficial effects:
compared with the prior art, the method firstly uses the TOCSY spectrum and the NOESY spectrum to simultaneously evaluate the similarity of the covalent structure and the space structure of the protein medicine, so that the structure evaluation is more comprehensive; secondly, the method comprehensively considers the chemical shift and the relative intensity change of all signals for quantitative analysis, so that the analysis structure is more accurate; finally, the method does not need to use professional computing software to carry out a large amount of time-consuming computing analysis, is simple and easy to implement, and is very suitable for popularization and application.
Drawings
FIG. 1 is a flow chart of quantitative assessment of structure of a protein drug in an embodiment of the present invention.
FIGS. 2A-2B are the results of covalent structure evaluation in the examples of the present invention.
Fig. 3A to 3D are results of spatial structure evaluation in the embodiment of the present invention.
Detailed Description
In order to make the aforementioned and other features and advantages of the invention more comprehensible, embodiments accompanied with figures are described in detail below.
The embodiment discloses a method for quantitatively evaluating the structure of a protein medicament based on a high-field nuclear magnetic resonance technology, and the sample adopted by the embodiment is recombinant human parathyroid hormone which is a protein medicament for treating paradoxical gland and bone metabolic diseases. The purpose of controlling the quality of the subsequent product is realized by comparing the covalent and spatial structures of the standard sample and the subsequent product. With the development of nuclear magnetic resonance hardware, especially the increase of instrument field intensity and the use of ultra-low temperature probes, the resolution and sensitivity of nuclear magnetic resonance experiments are greatly improved, and the nuclear magnetic resonance experiment device is widely applied to the research of various biomacromolecules. Nuclear magnetic resonance 2D 1 H- 1 The H TOCSY spectrum can measure the related signals of all hydrogen and hydrogen in the spin system, and can carry out the characterization of the covalent structure of the protein; and 2D 1 H- 1 H NOESY experiment can measure the space distance information of all hydrogen atoms and provide the information of the space structure of protein. Thus, the present invention acquires two-dimensional 2D using a high resolution and high sensitivity nuclear magnetic resonance method 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 The similarity of covalent and spatial structure of the standard and test samples can be assessed by H NOESY experiments and quantitative comparison of the results.
The method of the embodiment has a flowchart as shown in fig. 1, and includes the following specific operation steps:
1. sample preparation:
1.75 and 1.15mg of the standard and test samples were dissolved in 500. mu.L of pH 6.0 phosphate buffered solution containing 10% deuterium and internal standard DSS.
2. Sample data acquisition and data processing:
collecting high-field nuclear magnetic resonance 2D of a protein drug standard sample and a test sample on a 500MHz nuclear magnetic resonance instrument at the temperature of 298K 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 H NOESY spectra, mixing times for the experiments were 80ms and 200ms, respectively. And (3) processing the spectrogram by solvent pressing, adding a window function, Fourier transform, baseline phase calibration and linear prediction to obtain four high-quality and high-resolution spectrograms for comparison.
3. Quantitative evaluation of nuclear magnetic resonance spectrum:
2D 1 H- 1 the evaluation results of the H TOCSY spectra are shown in fig. 2A-2B, and fig. 2A is a comparison of the spectra of the chemical shifts of the fingerprint, which shows that the overall spectra overlap better. Marking the signals with chemical shift change, extracting corresponding chemical shifts, calculating average chemical shift difference by root mean square of two-dimensional chemical shift difference, making a histogram by using signal numbers and the average chemical shift difference as shown in figure 2B, wherein all the chemical shift differences in the histogram are less than 0.008ppm, which indicates that the covalent structures of the standard sample and the test sample are consistent.
2D 1 H- 1 The results of the evaluation of the H NOESY spectra are shown in FIGS. 3A to 3D, and FIG. 3A, FIG. 3B and FIG. 3C reflect the spatial information between the main chain amino hydrogen and the amino acid hydrocarbon, between the amino hydrogen and between the amino acid hydrocarbon, respectively. In view of the whole, the spectrograms of all the areas are better overlapped. Signals with large changes in chemical shift and signal intensity are labeled, the chemical shifts and intensities of these signals are extracted, and one signal with unchanged signal shift and intensity is selected as a reference (numbered 0) for calculating the relative intensity. Calculating an average chemical shift difference using a root mean square of the two-dimensional chemical shift differences; the intensities of all the varied signals were divided by the intensity of the reference signal to eliminate the overall intensity error of the two samples due to external conditions such as concentration, and then the deviation of the distance due to the relative intensity change was calculated according to the formula in the description of the above method, and then plotted as shown in fig. 3D. The chemical shift variation of all signals is less than 0.008ppm, the characteristic distance deviation exceeds a half of the displacement +/-2%, only four signals with the deviation exceeding +/-5% exist, the deviation is within +/-10%, the four signals are very weak, and the signal-to-noise ratio is poor. The spatial structure of the test sample and the standard sample are substantially identical in general.
In conclusion, the covalent and spatial structures of the standard and test samples were consistent.
The above-described embodiments are not intended to limit the present invention, and various modifications and changes may be made by those skilled in the art. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present application should be included in the scope of the claims of the present application.
Claims (10)
1. A method for quantitatively evaluating the structure of a protein drug based on a high-field nuclear magnetic resonance technology is characterized by comprising the following steps:
high-field nuclear magnetic resonance 2D for collecting protein drug standard sample and test sample 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 H NOESY spectrum, which is used for processing the spectrogram data and improving the quality and resolution of the spectrogram;
comparison target2D of quasi-and test samples 1 H- 1 H TOCSY spectrum, firstly marking the signal of difference of chemical shift in the fingerprint area of the spectrum, reading the chemical shift, then calculating the root mean square value of the two-dimensional chemical shift difference, and evaluating the similarity of the covalent structure of the protein drug standard sample and the test sample according to the root mean square value of the two-dimensional chemical shift difference;
comparing 2D of standard and test samples 1 H- 1 The H NOESY spectrum is characterized in that signals with changed chemical shift and intensity in NH-NH, NH-CH and CH-CH regions of the spectrum are marked, the chemical shift and the relative intensity of the signals are read, the root mean square value of two-dimensional chemical shift difference is calculated, the spatial distance difference of two samples based on the relative intensity of the signals is calculated, and the similarity of the spatial structures of the protein drug standard sample and the test sample is evaluated together according to the root mean square value and the spatial distance difference of the two-dimensional chemical shift difference.
2. The method of claim 1, wherein the following treatments are performed on the protein drug standard sample and the test sample in advance: the sample is dissolved in a buffer system without hydrogen with the pH value less than 7.5, and 10 percent of heavy water is added for field-locking shimming.
3. The method of claim 1, wherein the step of processing the spectrogram comprises: solvent pressing, addition of a window function, fourier transform, baseline phase calibration and linear prediction.
4. The method of claim 1, wherein 2D 1 H- 1 H TOCSY Spectrum and 2D 1 H- 1 H NOESY spectra were collected using different NMR instruments with ultra low temperature probes above 500MHz depending on the actual molecular weight of the sample.
5. The method of claim 1, wherein 2D 1 H- 1 The mixing time of the H TOCSY spectrum is set to be 80 ms; 2D 1 H- 1 When H NOESY spectra are mixedThe time is 50-200ms, and the specific mixing time is determined according to the molecular weight of the protein.
6. The method of claim 1, wherein the root mean square value of the two-dimensional chemical shift difference is calculated as
Wherein delta x And delta y The difference in chemical shift in the x and y dimensions, respectively.
7. The method of claim 1, wherein the relative intensity of the signal is equal to the ratio of the intensity of the label signal to the reference signal in the spectra, and the reference signal in the spectra of the two samples is the same signal in the two spectra.
8. The method of claim 1, wherein the signal of varying intensity is a NOE signal; the spatial distance difference of the two samples refers to the relative distance difference of the test sample relative to the standard sample, and the calculation formula is
I Sign board And I Measuring Relative intensities of NOE signals for the standard and test samples, respectively.
9. The method of claim 1, wherein 2D 1 H- 1 The fingerprint area of the H TOCSY spectrogram refers to a related signal area of amino hydrogen of a protein main chain and all hydrogen in residues, and the chemical shift range is (6-9 ppm, -2-6 ppm); 2D 1 H- 1 The chemical shift ranges of NH-NH, NH-CH and CH-CH regions of the H NOESY spectrum are (6-9 ppm ), (6-9 ppm, -2-6 ppm) and (-2-6 ppm ) regions with signals respectively.
10. The method of claim 1, wherein the condition that the covalent structure and the steric structure of the proteinaceous drug are identical is that: the two-dimensional chemical shift difference has a root mean square value of less than 0.008ppm and a spatial range difference of less than + -10% for all intensity signals.
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| 李双利;朱勤俊;刘买利;杨运煌;: "蛋白质分子核磁共振谱峰的特性及其化学位移归属", 波谱学杂志, no. 02, 15 June 2017 (2017-06-15) * |
| 胡蕴菲;金长文;: "蛋白质溶液结构及动力学的核磁共振研究", 波谱学杂志, no. 02, 15 June 2009 (2009-06-15) * |
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