CN103093100A - Building method of anthocyanin antioxidant activity three-dimensional quantitative structure-activity relationship model - Google Patents
Building method of anthocyanin antioxidant activity three-dimensional quantitative structure-activity relationship model Download PDFInfo
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Abstract
The invention relates to a building method of an anthocyanin antioxidant activity three-dimensional quantitative structure-activity relationship model. An anthocyanin antioxidant with a known activity is taken as a study object, a technology of three-dimensional quantitative structure-activity relationship is used, an anthocyanin antioxidant three-dimensional quantitative structure-activity relationship model is built, an accurate structure-activity relationship model is built through a molecular force field method and a molecular similarity coefficient analytical method for analyzing technologies of molecular conformation optimization, parameter optimization and the like. The building method of the anthocyanin antioxidant activity three-dimensional quantitative structure-activity relationship model can quickly predict activity value of an unknown activity compound, and can reasonably interpret the relation between the size of the nthocyanin antioxidant activity and the structure characteristics of the nthocyanin antioxidant activity.
Description
Technical field
The present invention relates to a kind of construction method and application of anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model, be specifically related to utilize the anthocyanin material of known activity to be research object, build the method for antioxidation activity three-dimensional quantitative structure activity relationship, and utilize the model that builds to carry out the prediction of unknown compound activity and the reasonable explaination of structure-activity relationship.
Background technology
Free radical is a kind of intermediate product that produces in the biosome vital movement.Body under normal circumstances, the generation of free radical and elimination are in mobile equilibrium, if in time remove but interior free yl produces too much or not, too much free radical will have destruction to body, cause the damage of human normal cell and tissue, thereby cause a lot of diseases, as angiocardiopathy, aging, tumour, senile dementia etc.
In view of the damage of excessive radical pair body, so must there be some can alleviate or eliminate the material of free radical harm, play inoxidizability, this class material is exactly antioxidant.
Antioxidant refers to that in broad terms all can directly remove free radical, or suppresses to start free chain reaction, stops free radical reaction, or can improve the compound of endogenous polyphenoils level.Antioxidant generally is divided into two classes by its source, and a class is synthetized oxidation preventive agent, and a class is natural.
Common synthetized oxidation preventive agent has BHT (BHT), BHA (cloves BHA), TBHQ (TBHQ) at present.The inoxidizability of synthetized oxidation preventive agent is very strong, but along with going deep into of people's understanding and research, these materials can damage human body, make the interpolation of synthetized oxidation preventive agent in food be very restricted, and become a research tendency so explore natural.
The material that can be used as natural of research mainly contains Polyphenols, vitamins, polysaccharide, terpene, flavonoids, polypeptide class etc. at present.These materials are all generally to derive from plant, and safety is nontoxic, is studied widely as the functional food trophic factors.
The three-dimensional quantitative structure activity relationship model is a kind of physicochemical property parameter or structural parameters by molecule, with mathematics and statistics means quantitative examination organic molecule and the method for the physiological correlations matter such as interaction of biomacromolecules, organic molecule absorb in vivo, distribution, metabolism, excretion.Now widely used three-dimensional quantitative structure activity relationship research method mainly contains comparison molecule position analytic approach (CoMFA) and molecular mimicry property coefficient analytic approach (CoMSIA).
Along with the development of science and technology and continually developing of theoretical calculating simulation softward, the research of structure-activity relationship has also obtained development significantly.Three-dimensional quantitative structure activity relationship is mainly the 3 D stereo conformation of having considered compound molecule, this is very crucial on the impact of activity on characterizing three-dimensional conformation, it can reflect molecule Stable conformation and bioactive relation under given conditions more accurately, disclose the active site of molecule, and then the mechanism of explaination activity relationship.Therefore structure activity study is just being brought into play more and more important effect aspect antioxidation activity.
Summary of the invention
The present invention is directed to prior art to the deficiency of antioxidant active mechanism explaination, a kind of construction method and application of anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model are provided.Described method is take the anthocyanin antioxidant of known activity and structure as research object, utilize the three-dimensional quantitative structure activity relationship technology, adopt the analyses of molecular force field method (CoMFA) and molecular mimicry property coefficient analytic approach (CoMSIA), set up anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model accurately by technology such as molecular conformation optimization, parameter optimizations.Constructed model can fast prediction the activity of unknown reactive compound, and can rationally explain the relation of anthocyanin antioxidation activity size and its architectural feature.
For achieving the above object, the present invention adopts following scheme:
A kind of construction method of anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model comprises the following steps:
(1) measure the antioxidation activity size of anthocyanin material, and be test set and training set with its random packet, index of biological activity adopts the negative logarithm of antioxidation activity to represent;
(2) use software analysis to obtain the three-D space structure of the compound in training set and test set, obtain the three-D space structure model of optimizing through Optimum configuration;
(3) the public rigid backbone of optimizing the three-D space structure model that obtains in the step (2) is for basic, and to carry out molecule superimposed as template for the molecule of antioxidation activity maximum in the training set;
(4) search superimposed rear compound field of force information on every side with Small-molecule probe and calculate field of force value;
(5) field of force information of step (4) acquisition and the biologically active value of the compound in training set are carried out the partial least square method recurrence, obtain anthocyanin material antioxidation activity three-dimensional quantitative structure activity relationship model.
Use software analysis to obtain the three-D space structure of compound in described step (2), described software refers to SYBYL-X1.2 software; Optimum configuration in described step (2) is to use the Tripos field of force to be optimized, and adds Gasteiger-H ü ckel electric charge, and the energy convergence is limited to 0.005kcal/mol, and maximum iteration time is 1000 times; The folding method that adopts in described step (3) is Align Database method; The Small-molecule probe that adopts in described step (4) is sp
3The carbon atom of hydridization; The field of force value of calculating in described step (4) is CoMFA or CoMSIA field of force value; In described step (5), the biologically active value of the compound in field of force information and training set is carried out partial least square method and return, with cross validation coefficient q
2Greater than 0.5, non-cross validation coefficient r
2Be the rationality of characterization model greater than 0.8.
In a better embodiment, described construction method comprises following concrete steps:
(1) according to design feature and the active size of aldehydes matter, to 25 anthocyanin material random packet, choose 18 compounds as training set, remaining 7 form test set (seeing Table 1); Index of biological activity adopts oxyradical receptivity (Oxygen Radical Absorption Capacity, ORAC) ORAC, and a great deal of (μ mole Trolox/mole) that namely is equivalent to Trolox calculates;
(2) molecule optimization: the three-D space structure that builds compound in training set and test set with the SYBYLX-1.2 analysis software.Select the Powell method under Tripos position, charge type is Gasteiger-H ü ckel, and the energy convergence is limited to 0.005kcal/mol, and maximum iteration time is 1000 times; Other parameters selection default values carry out molecule optimization, seek the Optimum configuration of each molecule;
(3) molecule is superimposed: obtain the Optimum configuration of each molecule after molecule optimization, choose in training set the highest active compound as template molecule, take phenyl ring as public skeleton, adopt Align Database method to carry out molecule superimposed;
(4) field of force energy calculates: utilize sp
3The carbon atom of hydridization is done the Small-molecule probe group, calculates the interaction energy of probe group and each molecule on each space networks lattice point, namely obtains superimposed rear compound field of force energy information on every side;
(5) model is set up: in the field of force obtained above energy value and training set, the biologically active value of compound is carried out the partial least square method recurrence, at first adopts the change method of taking out to carry out cross validation analysis (leave-one-out), obtains cross validation related coefficient q
2With best number of principal components n, then utilize the best number of principal components that obtains to carry out non-cross validation analysis (No-Validation), obtain anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model, with cross validation coefficient q
2Greater than 0.5, non-cross validation coefficient r
2Greater than 0.8 being the rationality of characterization model, q
2The ability that is worth higher expression activity analysis is stronger.
Advantage of the present invention is:
1, adopt SYBYL software, set up anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model by CoMFA and CoMSIA method, the model of foundation has predictive ability preferably.
2, utilize the three-dimensional quantitative structure activity relationship model of setting up, can well predict the activity of unknown compound, can rationally explain the anthocyanin antioxidant active mechanism.
Embodiment
Below by embodiment, the present invention is specifically described, but technical solution of the present invention is not limited to following cited embodiment.
Embodiment 1:
Choose 25 kinds of anthocyanin compounds (table 1) as research object, measure the ability that 25 kinds of materials are removed oxygen radical, take oxyradical receptivity (Oxygen Radical Absorption Capacity, ORAC) as index of biological activity; Choose at random 18 kinds as training set (table 1) in having measured 25 kinds of compounds of antioxidation activity, 7 kinds as test set, and 25 kinds of compounds are divided into groups; Under SYBYL X-1.2 software, draw the structural drawing of these 25 kinds of anthocyanin compounds; Select the Powell method under Tripos position, charge type is Gasteiger-H ü ckel, carries out molecule optimization, obtains the Optimum configuration of each molecule; Choose the highest active compound as template molecule (in table 1, compound 7) in the training set compound, selecting phenyl ring is public skeleton, and it is superimposed that employing Align Database method is carried out molecule; Calculating CoMFA field of force value comprises three-dimensional field effect and electrostatic field effect value, utilizes sp
3The carbon atom of hydridization is as the probe group, calculate on each space networks lattice point probe group respectively with the interaction energy of 18 molecules, this energy value is the field of force energy information that calculates; Adopt partial least square method that the activity value of three-dimensional field effect value and electrostatic field effect value and compound is returned, obtain cross validation coefficient q
2Value is 0.857, and best number of principal components is 4, non-cross validation coefficient r
2Value is 0.957, and standard deviation s is that 0.153, F test value is 73.267; Obtain anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship CoMFA model.Namely from the relation of three-dimensional field effect and electrostatic field effect consideration antioxidation activity and anthocyanin structure, utilize the field effect potentiometric map reasonable dismissal antioxidant active mechanism that obtains.By the prediction to 7 compound activity values in test set, the accuracy of model and predictive ability have preferably well been verified, referring to table 1.
Embodiment 2:
Choose 25 kinds of anthocyanin compounds as research object (table 1), measure the ability that 25 kinds of materials are removed oxygen radical, take oxyradical receptivity (Oxygen Radical Absorption Capacity, ORAC) as index of biological activity; Choose at random 18 kinds as training set in having measured 25 kinds of compounds of antioxidation activity, 7 kinds as test set; Under SYBYL X-1.2 software, draw the three-D space structure of each compound; Select the Powell method under Tripos position, charge type is Gasteiger-H ü ckel, and other parameters are carried out molecule optimization with embodiment 1, obtain the Optimum configuration of each molecule; The molecule Optimum configuration that draws is carried out superimposed, choose the highest active compound and do (in table 1, compound 7) and be template molecule in the training set compound, selecting phenyl ring is public skeleton, adopts Align Database method to carry out molecule superimposed; Calculating molecular mimicry property coefficient CoMSIA field of force value comprises three-dimensional field effect and electrostatic field effect value, hydrophobic field effect value, and hydrogen bond receptor field and hydrogen bond donor field effect value are utilized sp
3The carbon atom of hydridization is as the probe group, calculate on each space networks lattice point probe group respectively with the interaction energy of 18 molecules, this energy value is the field of force energy information that calculates; Adopt partial least square method that 5 effect field values are returned with the activity value of compound respectively, obtain cross validation coefficient q
2Value is 0.729, and best number of principal components is 4, non-cross validation coefficient r
2Value is 0.856, and standard deviation s is that 0.134, F test value is 19.247; Obtain anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship CoMSIA model, namely from three-dimensional field effect and electrostatic field effect, hydrophobic field effect, the relation of antioxidation activity and anthocyanin structure is considered in hydrogen bond receptor field and hydrogen bond donor field effect, the field effect potentiometric map reasonable dismissal antioxidation activity that utilization obtains and the relation of anthocyanin structure.At last by to the predicting of 7 compound activity values in test set, the accuracy of model and predictive ability have preferably well been verified, referring to table 1.
The molecular structure of table 1 anthocyanin and ORAC active testing value and predicted value
Annotate standby:
a, the test set compound
b, the template compound in training set
c, the ORAC value is calculated with the Trolox a great deal of, represents with μ mol Trolox/mol.
Other, Glc, glucoside (glucosyl group); Gal, galacoside (galactosyl); Ara, the arabinoside(aralino); Rut, rutinoside (rue glycosyl); Sam, sambubioside (mulberry cloth disaccharide base); Sop, sophoroside (sophorosyl); Cou-sam, sambubioside acyl with p-coumaric acid(is to coumaric acyl mulberry cloth disaccharide base); Cou-rut, rutinoside acyl with p-coumaric acid(is to coumaric acyl rue glycosyl); Cou-sop:sophoroside acyl with p-coumaric acid (to the coumaric acyl sophorosyl); Mal-glc, glucoside acyl with malonic acid (malonyl glucosyl group).
Claims (8)
1. the construction method of an anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model comprises the following steps:
(1) measure the antioxidation activity size of anthocyanin material, and be test set and training set with its random packet, index of biological activity adopts the negative logarithm of antioxidation activity to represent;
(2) use software analysis to obtain the three-D space structure of the compound in training set and test set, obtain the three-D space structure model of optimizing through Optimum configuration;
(3) the public rigid backbone of optimizing the three-D space structure model that obtains in the step (2) is for basic, and to carry out molecule superimposed as template for the molecule of antioxidation activity maximum in the training set;
(4) search superimposed rear compound field of force information on every side with Small-molecule probe and calculate field of force value;
(5) field of force information of step (4) acquisition and the biologically active value of the compound in training set are carried out the partial least square method recurrence, obtain anthocyanin material antioxidation activity three-dimensional quantitative structure activity relationship model.
2. construction method as claimed in claim 1, is characterized in that, uses software analysis to obtain the three-D space structure of compound in described step (2), and described software refers to SYBYL-X1.2 software.
3. construction method as claimed in claim 1, it is characterized in that, the Optimum configuration in described step (2) is to use the Tripos field of force to be optimized, and adds Gasteiger-H ü ckel electric charge, the energy convergence is limited to 0.005kcal/mol, and maximum iteration time is 1000 times.
4. construction method as claimed in claim 1, is characterized in that, the folding method that adopts in described step (3) is Align Database method.
5. construction method as claimed in claim 1, is characterized in that, the Small-molecule probe that adopts in described step (4) is sp
3The carbon atom of hydridization.
6. construction method as claimed in claim 1, is characterized in that, the field of force value of calculating in described step (4) is CoMFA or CoMSIA field of force value.
7. construction method as claimed in claim 1, is characterized in that, in described step (5), the biologically active value of the compound in field of force information and training set carried out partial least square method and return, with cross validation coefficient q
2Greater than 0.5, non-cross validation coefficient r
2Be the rationality of characterization model greater than 0.8.
8. described construction method as arbitrary in claim 1-7, wherein said method comprises following concrete steps:
(1) according to design feature and the active size of aldehydes matter, 25 anthocyanin material random packet in his-and-hers watches 1 are chosen 18 compounds as training set, and remaining 7 form test set; Index of biological activity adopts oxyradical receptivity ORAC to calculate;
(2) molecule optimization: the three-D space structure that builds compound in training set and test set with SYBYL X-1.2 analysis software.Select the Powell method under Tripos position, charge type is Gasteiger-H ü ckel, and the energy convergence is limited to 0.005kcal/mol, and maximum iteration time is 1000 times; Other parameters selection default values carry out molecule optimization, seek the Optimum configuration of each molecule;
(3) molecule is superimposed: obtain the Optimum configuration of each molecule after molecule optimization, choose in training set the highest active compound as template molecule, take phenyl ring as public skeleton, adopt Align Database method to carry out molecule superimposed;
(4) field of force energy calculates: utilize sp
3The carbon atom of hydridization is done the Small-molecule probe group, calculates the interaction energy of probe group and each molecule on each space networks lattice point, namely obtains superimposed rear compound field of force energy information on every side;
(5) model is set up: in the field of force obtained above energy value and training set, the biologically active value of compound is carried out the partial least square method recurrence, at first adopts the change method of taking out to carry out the cross validation analysis, obtains cross validation related coefficient q
2With best number of principal components n, then utilize the best number of principal components that obtains to carry out non-cross validation analysis, obtain anthocyanin antioxidant antioxidation activity three-dimensional quantitative structure activity relationship model, with cross validation coefficient q
2Greater than 0.5, non-cross validation coefficient r
2Greater than 0.8 being the rationality of characterization model, q
2The ability that is worth higher expression activity analysis is stronger.
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| CN108573123A (en) * | 2018-05-09 | 2018-09-25 | 深圳晶泰科技有限公司 | Medicine crystal structure panorama analytical method system and its panorama analytical method method |
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN103714266A (en) * | 2013-12-31 | 2014-04-09 | 长沙理工大学 | Construction method of three-dimensional quantitative structure-activity relationship model of food-borne polypeptide antioxidant activity |
| CN103714266B (en) * | 2013-12-31 | 2016-06-01 | 长沙理工大学 | Construction method of three-dimensional quantitative structure-activity relationship model of food-borne polypeptide antioxidant activity |
| CN108573123A (en) * | 2018-05-09 | 2018-09-25 | 深圳晶泰科技有限公司 | Medicine crystal structure panorama analytical method system and its panorama analytical method method |
| CN108573123B (en) * | 2018-05-09 | 2021-07-30 | 深圳晶泰科技有限公司 | Panoramic analysis system and panoramic analysis method for medicine crystal structure |
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