A novel three-dimensional holographic vector of atomic interaction field（3D-HoVAIF） was used to describe the chemical structures of 23 benzoxazinone derivatives as antithrombotic drugs.Here a quantitative structure ...A novel three-dimensional holographic vector of atomic interaction field（3D-HoVAIF） was used to describe the chemical structures of 23 benzoxazinone derivatives as antithrombotic drugs.Here a quantitative structure activity relationship（QSAR） model was built by partial least-squares（PLS） regression.The estimation stability and prediction ability of the model were strictly analyzed by both internal and external validations.The correlation coefficients of established PLS model,leave-one-out（LOO） cross-validation,and predicted values versus experimental ones of external samples were R2=0.899,RCV2=0.854 and Qext2=0.868,respectively.These values indicated that the built PLS model had both favorable estimation stability and good prediction capabilities.Furthermore,the satisfactory results showed that 3D-HoVAIF could preferably express the information related to the biological activity of benzoxazinone derivatives.展开更多
It is important to calibrate micro-parameters for applying partied flow code(PFC)to study mechanical characteristics and failure mechanism of rock materials.Uniform design method is firstly adopted to determine the mi...It is important to calibrate micro-parameters for applying partied flow code(PFC)to study mechanical characteristics and failure mechanism of rock materials.Uniform design method is firstly adopted to determine the microscopic parameters of parallel-bonded particle model for three-dimensional discrete element particle flow code(PFC3D).Variation ranges of microscopic of the microscopic parameters are created by analyzing the effects of microscopic parameters on macroscopic parameters(elastic modulus E,Poisson ratio v,uniaxial compressive strengthσc,and ratio of crack initial stress to uniaxial compressive strengthσci/σc)in order to obtain the actual uniform design talbe.The calculation equations of the microscopic and macroscopic parameters of rock materials can be established by the actual uniform design table and the regression analysis and thus the PFC3D microscopic parameters can be quantitatively determined.The PFC3D simulated results of the intact and pre-cracked rock specimens under uniaxial and triaxial compressions(including the macroscopic mechanical parameters,stress−strain curves and failure process)are in good agreement with experimental results,which can prove the validity of the calculation equations of microscopic and macroscopic parameters.展开更多
Study on the quantitative structure-activity relationship （QSAR） of 26 compounds, N-[5-（2-furanyl）-2-methyl-4-oxo-4H-thieno[2,3-d]pyrimidin-3-yl]-carboxamide and 3-substituted- 5-（2-furanyl）-2-methyl-3H-thieno[2...Study on the quantitative structure-activity relationship （QSAR） of 26 compounds, N-[5-（2-furanyl）-2-methyl-4-oxo-4H-thieno[2,3-d]pyrimidin-3-yl]-carboxamide and 3-substituted- 5-（2-furanyl）-2-methyl-3H-thieno[2,3-d]pyrimidin-4-ones, with three-dimensional holographic vector of atomic interaction field （3D-HoVAIF） was carried out. SMR-PLS QSAR models have been created and good correlation coefficients and cross-validated correlation coefficients were obtained. The result shows that the models have good prediction capability and favorable stability and the 3D-HoVAIF is applicable to the molecular structural characterization and biological activity prediction.展开更多
Based on the obtained data of half-lives（t1/2） for 31 polychlorinated biphenyl congeners（PCBs）, 3D quantitative structure-activity relationship（QSAR） pharmacophore was used to establish a 3D QSAR model to predic...Based on the obtained data of half-lives（t1/2） for 31 polychlorinated biphenyl congeners（PCBs）, 3D quantitative structure-activity relationship（QSAR） pharmacophore was used to establish a 3D QSAR model to predict the t1/2 values of the remaining 178 PCBs, using the structural parameters as independent variables and lgt1/2 values as the dependent variable. Among this process, the whole data set（31 compounds） was divided into a training set（24 compounds） for model generation and a test set（7 compounds） for model validation. Then, the full factor experimental design was used to research the potential second-order interactional effect between different substituent positions, obtaining the final regulation scheme for PCB. At last, a 3D QSAR pharmacophore model was established to validate the reasonable regulation targeting typical PCB with respect to half-lives and thermostability. As a result, the cross-validation correlation coefficient（q2） obtained by the 3D QSAR model was 0.845（〉0.5） and the coefficient of determination（r2） obtained was 0.936（〉0.9）, indicating that the models were robust and predictive. CoMSIA analyses upon steric, electrostatic and hydrophobic fields were 0.7%, 85.9%, and 13.4%, respectively. The electrostatic field was determined to be a primary factor governing the tt/2. From CoMSIA contour maps, tl/2 increased when substi- tuents possessed electropositive groups at the 2＇-, 3-, Y-, 5- and 5＇- positions and electronegative groups at the 3-, 3＇-, 5-, 6- and 6＇- positions, which could increase the PCB stability in transformer insulation oil. Modification of two typical PCB congeners（PCB-77 and PCB-81） showed that the lgtl/2 for three selected modified compounds increased by 13%（average ratio） compared with that of each congener and the thermostability of them were higher, validating the reasonability of the regulatory scheme obtained from the 3D QSAR model. These results are expected to be beneficial in predicting tl/2 values of PCB homologues and derivatives and in providing a theoretical foundation for further elucidation of the stability of PCBs.展开更多
20 Typical flavonoids were selected for study on the interaction between them and PIM-1 kinase with the comparative molecular field analysis method（CoMFA） as well as the comparative molecular similarity index analys...20 Typical flavonoids were selected for study on the interaction between them and PIM-1 kinase with the comparative molecular field analysis method（CoMFA） as well as the comparative molecular similarity index analysis method（CoMSIA） based on molecule docking.3D-QSAR models between these flavonoids and receptor PIM-1 kinase were established.The obtained optimal cross-validation correlation coefficient Q2 for CoMFA model was 0.582,and the non-cross-validation correlation coefficient R2 was 0.955;the corresponding values for CoMSIA model were 0.790 and 0.974,respectively.These two models showed fairly fine stability and predictive ability.In addition,molecule docking results revealed the key residues in the receptor cavity and their specific action ways with flavonoids.展开更多
Cancer is one of the most serious issues in human life.Blocking programmed cell death protein 1 and programmed death ligand-1(PD-L1)pathway is one of the great innovations in the last few years,a few numbers of inhibi...Cancer is one of the most serious issues in human life.Blocking programmed cell death protein 1 and programmed death ligand-1(PD-L1)pathway is one of the great innovations in the last few years,a few numbers of inhibitors can be able to block it.(2-Methyl-3-biphenylyl)methanol derivative is one of them.Here,the quantitative structure-activity relationship(QSAR)established twenty(2-methyl-3-biphenylyl)methanol derivatives as the programmed death ligand-1 inhibitors.Density functional theory at the B3LPY/6-31+G(d,p)level was employed to study the chemical structure and properties of the chosen compounds.Highest occupied molecular orbital energy EHOMO,lowest unoccupied molecular orbital energy ELUMO,total energy ET,dipole moment DM,absolute hardnessη,absolute electronegativityχ,softness S,electrophilicityω,energy gap?E,etc.,were observed and determined.Principal component analysis(PCA),multiple linear regression(MLR)and multiple nonlinear regression(MNLR)analysis were carried out to establish the QSAR.The proposed quantitative models and interpreted outcomes of the compounds were based on statistical analysis.Statistical results of MLR and MNLR exhibited the coefficient R^2 was 0.661 and 0.758,respectively.Leave-one-out cross-validation,r_m^2 metric,r_m^2 test,and"Golbraikh&Tropsha’s criteria"analyses were applied for the validation of MLR and MNLR,which indicate two models are statistically significant and well stable with data variation in the external validation towards PD-L1.The obtained results showed that the MNLR model predicts the bioactivity more accurately than MLR,and it may be helpful and supporting for evaluation of the biological activity of PD-L1 inhibitors.展开更多
Considering atomic property vector and atomic correlative function, the 3-dimensional structural vector of atomic property correlation （3D-VAPC）, a novel descriptor,is defined to characterize a 3-dimensional molecul...Considering atomic property vector and atomic correlative function, the 3-dimensional structural vector of atomic property correlation （3D-VAPC）, a novel descriptor,is defined to characterize a 3-dimensional molecular structure by introducing self-adaptability regulation mechanism and the idea of orientating to customers. Characterizing the structures of 25 bisphenol A compounds by this vector, the QSAR models of three kinds of estrogen activities （ER affinities, gene induction and cell proliferation） have high multiple correlation coefficient （Rcum^2=0.933, 0.813, 0.959） and cross verification coefficient （Qcum^2=0.847, 0.953, 0.798） by support vector machine （SVM）, which suits for nonlinear circumstances. The above results show that the models successfully express the correlation between structure and three kinds of estrogen activities. Therefore, 3D-VAPC exactly reflects the molecular structural information and SVM method correctly describes the correlation between information and property of the compounds.展开更多
Canceling grids accommodating probes in comparative molecular field analysis (CoMFA), the idea of flexibleness is introduced into the CoMFA, and in combination with swarm intelligent algorithm which attempts to optimi...Canceling grids accommodating probes in comparative molecular field analysis (CoMFA), the idea of flexibleness is introduced into the CoMFA, and in combination with swarm intelligent algorithm which attempts to optimize distributions of diverse probes around drug molecules, a new 3D-QSAR method is proposed in this context as flexible comparative molecular field analysis (FCoMFA). In preliminary at-tempts to performing QSAR studies on 47 glycogen phosphorylase inhibitors, FCoMFA is employed and confirmed to be potent to exploring ligand-receptor interaction manners at active positions and thus to generating stable and predictable models. Simultaneously by an intuitive graphics regarding probe distribution patterns, impacts of different substituted groups on activities is also given an insight into.展开更多
A three-dimensional quantitative structure-activity relationship(3D-QSAR)model based on the fuzzy membership function method was developed in this study,and then the model was applied to the molecular design of the en...A three-dimensional quantitative structure-activity relationship(3D-QSAR)model based on the fuzzy membership function method was developed in this study,and then the model was applied to the molecular design of the enhanced comprehensive activities(insulation/flame retardancy)of polybrominated diphenyl ethers(PBDEs)considering their environmental behavior control,to develop environmental-friendly PBDE derivatives with outstanding functionality.Firstly,a fuzzy membership function method was employed to characterize the evaluation values of comprehensive activities of the functional properties of PBDEs based on the 3D-QSAR model.Secondly,a comprehensive activity 3D-QSAR model(CoMFA)of the functional properties of PBDEs was established,which demonstrated robustness and good predictive ability.Thirdly,a molecular modification scheme was designed to enhance the comprehensive activity of the functional properties of PBDEs considering the PBDE homologs BDE-138,BDE-183,and BDE-209 as target molecules.The resulting information indicated that the four PBDE derivatives with significantly enhanced functional properties,such as passing screening for toxicity,bioconcentration,migration,and biodegradability assessments with environmentally friendly results,were successfully designed(43.57%-82.14%enhancement).Finally,the mechanism analysis indicated that the enhanced functional properties of the modified PBDE derivatives were significantly related to the substitution positions and substitution groups of PBDEs.展开更多
5-Substituted benzylidene 3-acylthiotetronic acids are antifungal.A series of 3-acylthiotetronic acid derivatives with varying substitutions at the 5-position were designed,synthesized,and characterized,based on the b...5-Substituted benzylidene 3-acylthiotetronic acids are antifungal.A series of 3-acylthiotetronic acid derivatives with varying substitutions at the 5-position were designed,synthesized,and characterized,based on the binding pose of 3-acyl thiolactone with the protein C171Q KasA.Fungicidal activities of these compounds were screened against Valsa Mali,Curvularia lunata,Fusarium graminearum,and Fusarium oxysporum f.sp.lycopersici.Most target compounds exhibited excellent fungicidal activities against target fungi at the concentration of 50μg·mL-1.Compounds 11c and 11i displayed the highest activity with a broad spectrum.The median effective concentration(EC50)values of 11c and 11i were 1.9–10.7 and 3.1–7.8μg·mL-1,respectively,against the tested fungi,while the EC50 values of the fungicides azoxystrobin,carbendazim,and fluopyram were respectively 0.30,4.22,and>50μg·mL-1 against V.Mali;6.7,41.7,and 0.18μg·mL-1 against C.lunata;22.4,0.42,and 0.43μg·mL-1 against F.graminearum;and 4.3,0.12,and>50μg·mL-1 against F.oxysporum f.sp.lycopersici.The structures and activities of the target compounds against C.lunata were analyzed to obtain a statistically significant comparative molecular field analysis(CoMFA)model with high prediction abilities(q2=0.9816,r2=0.8060),and its reliability was verified.The different substituents on the benzylidene at the 5-position had significant effects on the activity,while the introduction of a halogen atom at the benzene ring of benzylidene was able to improve the activity against the tested fungi.展开更多
The quantitative structure-activity relationship （QSAR） of 30 acylthiourea analogues was studied by using a three-dimensional holographic vector of atomic interaction field （3D-HoVAIF） to describe their chemical s...The quantitative structure-activity relationship （QSAR） of 30 acylthiourea analogues was studied by using a three-dimensional holographic vector of atomic interaction field （3D-HoVAIF） to describe their chemical structures. The descriptors obtained were screened by stepwise multiple regression （SMR） and a partial least-squares （PLS） regression model was built. The correlation coefficient r^2 of the established model and Leave-One-Out （LOO） Cross-Validation （CV） correlation coefficient q^2 are 0.624 and 0.409, respectively. The model has favorable stability and good prediction capability, and further QSAR analysis showed that hydrophobic interaction has the most important effect on the activity of acylthiourea analogue and 3D-HoVAIF was applicable to the molecular structural characterization and biologicalactivity prediction.展开更多
Twenty-seven novel pyrrolidine-2,4-dione derivatives containing N-substituted phenylhydrazine moiety were synthesized. Their structures were confirmed by IH NMR, 13C NMR and MS. The half effective concentration （ECs0...Twenty-seven novel pyrrolidine-2,4-dione derivatives containing N-substituted phenylhydrazine moiety were synthesized. Their structures were confirmed by IH NMR, 13C NMR and MS. The half effective concentration （ECs0） values of the title compounds against the phytopathogenic fungi Rhizoctonia cerealis were evaluated. Com- pounds 61 and 6q displayed good bioactivity with EC50 values of 1.626 and 2.043 μg/mL, respectively. The 3D quantitative structure activity relationship（3D-QSAR） model of CoMFA was established with reliable cross-validated correlation coefficient q2 value of 0.585 and Noncross-validated correlation coefficient r2 value of 0.971. This model provided a tool for guiding further design and synthesis of novel pyrrolidine-2,4-dione derivatives with high fungicidal activity.展开更多
A three-dimensional quantitative structure-activity relationship(3 D-QSAR) study was conducted to analyze the A1 AR density(Bmax) of 56 3-aroyl-5-substituted thiophene derivatives(ASTDs) in human A1 Chinese hamster ov...A three-dimensional quantitative structure-activity relationship(3 D-QSAR) study was conducted to analyze the A1 AR density(Bmax) of 56 3-aroyl-5-substituted thiophene derivatives(ASTDs) in human A1 Chinese hamster ovary(hA1 CHO) membranes by the comparative molecular field analysis(CoMFA) method. A training set of 45 compounds was used to establish the predictive model, which was verified by the test set of 17 compounds containing template molecule and 5 newly designed molecules. The cross-validation(R2 cv) and non-cross-validation(R2) coefficients of the training set were 0.655 and 0.959, respectively. The model was used to predict the activities of the compounds of the training and test sets, and the results indicated that the models had strong stability and good prediction ability. According to model analysis, the contribution of steric and electrostatic fields was 51.4% and 48.6%, respectively. Based on the 3 D contour maps, five excellent ASTDs agonists were designed, which need to be further verified by biomedical experiments.展开更多
Topomer comparative molecular field analysis(Topomer Co MFA)and holographic quantitative structure-activity relationship(HQSAR)for 1302,5-diketopiperazine derivatives were used to build a three-dimensional quantitativ...Topomer comparative molecular field analysis(Topomer Co MFA)and holographic quantitative structure-activity relationship(HQSAR)for 1302,5-diketopiperazine derivatives were used to build a three-dimensional quantitative structure-activity relationship(3D-QSAR)model.The results show that the models have high predictive ability.For Topomer CoMFA,the cross-validated q^2 value is 0.710 and the non-cross-validated r^2 value is 0.834.The most effective HQSAR model shows that the cross-validation q^2 value is 0.700,the non-cross-validated r^2 value is 0.815,and the best hologram length value is 353 using connections and bonds as fragment distinctions.50 highly active 2,5-diketopiperazine derivatives were designed based on the three-dimensional equipotential map and HQSAR color code map.Finally,the molecular docking method was also used to study the interactions of these new molecules by docking the ligands into the diketopiperazine active site,which revealed the likely bioactive conformations.This study showed that there are extensive interactions between the new molecule and Arg156,Arg122 residues in the active site of diketopiperazine.These results provide useful insights for the design of potent of the new 2,5-diketopiperazine derivatives.展开更多
28 kinds of carotenoids are studied to reveal the key parameters and regulation on the singlet oxygen quenching rate.First,the quantum chemistry parameters of carotenoids calculated by Gaussian software combined with ...28 kinds of carotenoids are studied to reveal the key parameters and regulation on the singlet oxygen quenching rate.First,the quantum chemistry parameters of carotenoids calculated by Gaussian software combined with substitution parameters were used to construct the quantitative structure-activity relationship model(QSAR)of the singlet oxygen quenching rate of carotenoids.The key parameters affecting the antioxidant activity of carotenoids are revealed,and the data predicted via the QSAR model were provided for subsequent research.Then,a three-dimensional(3D)pharmacophore model was used to regulate and modify the antioxidant activity of carotenoids.The correlation coefficients of the modeling group(R2)and verification group(Rpre2)of the established QSAR model were 0.945 and 0.916,respectively,which can be used for the analysis of antioxidant activity of carotenoids;the antioxidant activity of carotenoids can be significantly regulated by the number of conjugated C=C bonds,the energy difference between frontier molecular orbitals and the partial Mulliken charge in C1 and theπ···π*excitation energy E(s);the antioxidant activity of carotenoids can be effectively regulated by the hydrogen bond acceptor pharmacophores on both sides of the conjugated C=C bonds and the hydrophobic groups on the conjugated C=C bond;the hydrophobic substituents attached to conjugated C=C bonds can effectively improve the singlet oxygen quenching rate of carotenoids.展开更多
基金supported by the Natural Science Foundation of Shaanxi Province (2009JQ2005)Foundation of Educational Commission of Shaanxi Province (09JK358) Graduate Innovation Fund of Shaanxi University of Science and Technology
文摘A novel three-dimensional holographic vector of atomic interaction field（3D-HoVAIF） was used to describe the chemical structures of 23 benzoxazinone derivatives as antithrombotic drugs.Here a quantitative structure activity relationship（QSAR） model was built by partial least-squares（PLS） regression.The estimation stability and prediction ability of the model were strictly analyzed by both internal and external validations.The correlation coefficients of established PLS model,leave-one-out（LOO） cross-validation,and predicted values versus experimental ones of external samples were R2=0.899,RCV2=0.854 and Qext2=0.868,respectively.These values indicated that the built PLS model had both favorable estimation stability and good prediction capabilities.Furthermore,the satisfactory results showed that 3D-HoVAIF could preferably express the information related to the biological activity of benzoxazinone derivatives.
基金Projects(51474251,51874351)supported by the National Natural Science Foundation,China。
文摘It is important to calibrate micro-parameters for applying partied flow code(PFC)to study mechanical characteristics and failure mechanism of rock materials.Uniform design method is firstly adopted to determine the microscopic parameters of parallel-bonded particle model for three-dimensional discrete element particle flow code(PFC3D).Variation ranges of microscopic of the microscopic parameters are created by analyzing the effects of microscopic parameters on macroscopic parameters(elastic modulus E,Poisson ratio v,uniaxial compressive strengthσc,and ratio of crack initial stress to uniaxial compressive strengthσci/σc)in order to obtain the actual uniform design talbe.The calculation equations of the microscopic and macroscopic parameters of rock materials can be established by the actual uniform design table and the regression analysis and thus the PFC3D microscopic parameters can be quantitatively determined.The PFC3D simulated results of the intact and pre-cracked rock specimens under uniaxial and triaxial compressions(including the macroscopic mechanical parameters,stress−strain curves and failure process)are in good agreement with experimental results,which can prove the validity of the calculation equations of microscopic and macroscopic parameters.
基金Supported by the Fund of National High Technology Research and Development Program (863 Program, No. 2006AA02Z312)
文摘Study on the quantitative structure-activity relationship （QSAR） of 26 compounds, N-[5-（2-furanyl）-2-methyl-4-oxo-4H-thieno[2,3-d]pyrimidin-3-yl]-carboxamide and 3-substituted- 5-（2-furanyl）-2-methyl-3H-thieno[2,3-d]pyrimidin-4-ones, with three-dimensional holographic vector of atomic interaction field （3D-HoVAIF） was carried out. SMR-PLS QSAR models have been created and good correlation coefficients and cross-validated correlation coefficients were obtained. The result shows that the models have good prediction capability and favorable stability and the 3D-HoVAIF is applicable to the molecular structural characterization and biological activity prediction.
文摘Based on the obtained data of half-lives（t1/2） for 31 polychlorinated biphenyl congeners（PCBs）, 3D quantitative structure-activity relationship（QSAR） pharmacophore was used to establish a 3D QSAR model to predict the t1/2 values of the remaining 178 PCBs, using the structural parameters as independent variables and lgt1/2 values as the dependent variable. Among this process, the whole data set（31 compounds） was divided into a training set（24 compounds） for model generation and a test set（7 compounds） for model validation. Then, the full factor experimental design was used to research the potential second-order interactional effect between different substituent positions, obtaining the final regulation scheme for PCB. At last, a 3D QSAR pharmacophore model was established to validate the reasonable regulation targeting typical PCB with respect to half-lives and thermostability. As a result, the cross-validation correlation coefficient（q2） obtained by the 3D QSAR model was 0.845（〉0.5） and the coefficient of determination（r2） obtained was 0.936（〉0.9）, indicating that the models were robust and predictive. CoMSIA analyses upon steric, electrostatic and hydrophobic fields were 0.7%, 85.9%, and 13.4%, respectively. The electrostatic field was determined to be a primary factor governing the tt/2. From CoMSIA contour maps, tl/2 increased when substi- tuents possessed electropositive groups at the 2＇-, 3-, Y-, 5- and 5＇- positions and electronegative groups at the 3-, 3＇-, 5-, 6- and 6＇- positions, which could increase the PCB stability in transformer insulation oil. Modification of two typical PCB congeners（PCB-77 and PCB-81） showed that the lgtl/2 for three selected modified compounds increased by 13%（average ratio） compared with that of each congener and the thermostability of them were higher, validating the reasonability of the regulatory scheme obtained from the 3D QSAR model. These results are expected to be beneficial in predicting tl/2 values of PCB homologues and derivatives and in providing a theoretical foundation for further elucidation of the stability of PCBs.
基金Sponsored by the National Natural Science Foundation of China (No. 20737001,20977046)the National Basic Research Program of China (No. 2009CB42160-4)
文摘20 Typical flavonoids were selected for study on the interaction between them and PIM-1 kinase with the comparative molecular field analysis method（CoMFA） as well as the comparative molecular similarity index analysis method（CoMSIA） based on molecule docking.3D-QSAR models between these flavonoids and receptor PIM-1 kinase were established.The obtained optimal cross-validation correlation coefficient Q2 for CoMFA model was 0.582,and the non-cross-validation correlation coefficient R2 was 0.955;the corresponding values for CoMSIA model were 0.790 and 0.974,respectively.These two models showed fairly fine stability and predictive ability.In addition,molecule docking results revealed the key residues in the receptor cavity and their specific action ways with flavonoids.
基金the Natural Science Foundation of Jiangsu Province(BK20181128)333 Project of Jiangsu Province(BRA2016518)Jiangsu Provincial Medical Youth Talent(QNRC2016626)。
文摘Cancer is one of the most serious issues in human life.Blocking programmed cell death protein 1 and programmed death ligand-1(PD-L1)pathway is one of the great innovations in the last few years,a few numbers of inhibitors can be able to block it.(2-Methyl-3-biphenylyl)methanol derivative is one of them.Here,the quantitative structure-activity relationship(QSAR)established twenty(2-methyl-3-biphenylyl)methanol derivatives as the programmed death ligand-1 inhibitors.Density functional theory at the B3LPY/6-31+G(d,p)level was employed to study the chemical structure and properties of the chosen compounds.Highest occupied molecular orbital energy EHOMO,lowest unoccupied molecular orbital energy ELUMO,total energy ET,dipole moment DM,absolute hardnessη,absolute electronegativityχ,softness S,electrophilicityω,energy gap?E,etc.,were observed and determined.Principal component analysis(PCA),multiple linear regression(MLR)and multiple nonlinear regression(MNLR)analysis were carried out to establish the QSAR.The proposed quantitative models and interpreted outcomes of the compounds were based on statistical analysis.Statistical results of MLR and MNLR exhibited the coefficient R^2 was 0.661 and 0.758,respectively.Leave-one-out cross-validation,r_m^2 metric,r_m^2 test,and"Golbraikh&Tropsha’s criteria"analyses were applied for the validation of MLR and MNLR,which indicate two models are statistically significant and well stable with data variation in the external validation towards PD-L1.The obtained results showed that the MNLR model predicts the bioactivity more accurately than MLR,and it may be helpful and supporting for evaluation of the biological activity of PD-L1 inhibitors.
基金This work was supported by the Natural Science Foundation of CQ CSTC (No. 2006BB5177)
文摘Considering atomic property vector and atomic correlative function, the 3-dimensional structural vector of atomic property correlation （3D-VAPC）, a novel descriptor,is defined to characterize a 3-dimensional molecular structure by introducing self-adaptability regulation mechanism and the idea of orientating to customers. Characterizing the structures of 25 bisphenol A compounds by this vector, the QSAR models of three kinds of estrogen activities （ER affinities, gene induction and cell proliferation） have high multiple correlation coefficient （Rcum^2=0.933, 0.813, 0.959） and cross verification coefficient （Qcum^2=0.847, 0.953, 0.798） by support vector machine （SVM）, which suits for nonlinear circumstances. The above results show that the models successfully express the correlation between structure and three kinds of estrogen activities. Therefore, 3D-VAPC exactly reflects the molecular structural information and SVM method correctly describes the correlation between information and property of the compounds.
基金Supported by National High Technology (863) Program (Grant No. 2006AA02Z312)the State Key Laboratory of Chemo/Biosensing and Chemometrics Foundation (Grant No. 0501201)Chongqing University Innovation Fund (Grant No. 030506)
文摘Canceling grids accommodating probes in comparative molecular field analysis (CoMFA), the idea of flexibleness is introduced into the CoMFA, and in combination with swarm intelligent algorithm which attempts to optimize distributions of diverse probes around drug molecules, a new 3D-QSAR method is proposed in this context as flexible comparative molecular field analysis (FCoMFA). In preliminary at-tempts to performing QSAR studies on 47 glycogen phosphorylase inhibitors, FCoMFA is employed and confirmed to be potent to exploring ligand-receptor interaction manners at active positions and thus to generating stable and predictable models. Simultaneously by an intuitive graphics regarding probe distribution patterns, impacts of different substituted groups on activities is also given an insight into.
基金This work was supported by the Key Projects in the National Science&Technology Pillar Program in the Eleventh Five-year Plan Period of China(No.2008BAC43B01)the Fundamental Research Funds for the Central Universities of China(No.2017XS058).
文摘A three-dimensional quantitative structure-activity relationship(3D-QSAR)model based on the fuzzy membership function method was developed in this study,and then the model was applied to the molecular design of the enhanced comprehensive activities(insulation/flame retardancy)of polybrominated diphenyl ethers(PBDEs)considering their environmental behavior control,to develop environmental-friendly PBDE derivatives with outstanding functionality.Firstly,a fuzzy membership function method was employed to characterize the evaluation values of comprehensive activities of the functional properties of PBDEs based on the 3D-QSAR model.Secondly,a comprehensive activity 3D-QSAR model(CoMFA)of the functional properties of PBDEs was established,which demonstrated robustness and good predictive ability.Thirdly,a molecular modification scheme was designed to enhance the comprehensive activity of the functional properties of PBDEs considering the PBDE homologs BDE-138,BDE-183,and BDE-209 as target molecules.The resulting information indicated that the four PBDE derivatives with significantly enhanced functional properties,such as passing screening for toxicity,bioconcentration,migration,and biodegradability assessments with environmentally friendly results,were successfully designed(43.57%-82.14%enhancement).Finally,the mechanism analysis indicated that the enhanced functional properties of the modified PBDE derivatives were significantly related to the substitution positions and substitution groups of PBDEs.
基金This work was financially supported in part by the National Natural Science Foundation of China(31901906)the Opening Project of Shanghai Key Laboratory of Chemical Biology,the Natural Science Foundation of Anhui Province,China(1808085QC71)+1 种基金the Natural Science Foundation of Anhui Education Department(KJ2016A834)the US Department of Agriculture(USDA:HAW5032-R).
文摘5-Substituted benzylidene 3-acylthiotetronic acids are antifungal.A series of 3-acylthiotetronic acid derivatives with varying substitutions at the 5-position were designed,synthesized,and characterized,based on the binding pose of 3-acyl thiolactone with the protein C171Q KasA.Fungicidal activities of these compounds were screened against Valsa Mali,Curvularia lunata,Fusarium graminearum,and Fusarium oxysporum f.sp.lycopersici.Most target compounds exhibited excellent fungicidal activities against target fungi at the concentration of 50μg·mL-1.Compounds 11c and 11i displayed the highest activity with a broad spectrum.The median effective concentration(EC50)values of 11c and 11i were 1.9–10.7 and 3.1–7.8μg·mL-1,respectively,against the tested fungi,while the EC50 values of the fungicides azoxystrobin,carbendazim,and fluopyram were respectively 0.30,4.22,and>50μg·mL-1 against V.Mali;6.7,41.7,and 0.18μg·mL-1 against C.lunata;22.4,0.42,and 0.43μg·mL-1 against F.graminearum;and 4.3,0.12,and>50μg·mL-1 against F.oxysporum f.sp.lycopersici.The structures and activities of the target compounds against C.lunata were analyzed to obtain a statistically significant comparative molecular field analysis(CoMFA)model with high prediction abilities(q2=0.9816,r2=0.8060),and its reliability was verified.The different substituents on the benzylidene at the 5-position had significant effects on the activity,while the introduction of a halogen atom at the benzene ring of benzylidene was able to improve the activity against the tested fungi.
基金supported by the National High-tech Research Program (the "863" Program, No. 2006AA02Z312)Innovative Group Program for Graduates of Chongqing University, Science and Innovation Fund (No. 200711C1A0010260)
文摘The quantitative structure-activity relationship （QSAR） of 30 acylthiourea analogues was studied by using a three-dimensional holographic vector of atomic interaction field （3D-HoVAIF） to describe their chemical structures. The descriptors obtained were screened by stepwise multiple regression （SMR） and a partial least-squares （PLS） regression model was built. The correlation coefficient r^2 of the established model and Leave-One-Out （LOO） Cross-Validation （CV） correlation coefficient q^2 are 0.624 and 0.409, respectively. The model has favorable stability and good prediction capability, and further QSAR analysis showed that hydrophobic interaction has the most important effect on the activity of acylthiourea analogue and 3D-HoVAIF was applicable to the molecular structural characterization and biologicalactivity prediction.
基金Supported by the National High Technology Research and Development Program of China（No.2011AA10A206）, the National Key Technologies R＆D Program of China（No.2011BAE06B04）, the Science ＆ Technology Pillar Program of Jiangsu Province, China（No.BE2012371）, the National Natural Science Foundation of China（No.31171889） and the Fundamental Research Funds for the Central Universities of China（No.KYZ201223）.
文摘Twenty-seven novel pyrrolidine-2,4-dione derivatives containing N-substituted phenylhydrazine moiety were synthesized. Their structures were confirmed by IH NMR, 13C NMR and MS. The half effective concentration （ECs0） values of the title compounds against the phytopathogenic fungi Rhizoctonia cerealis were evaluated. Com- pounds 61 and 6q displayed good bioactivity with EC50 values of 1.626 and 2.043 μg/mL, respectively. The 3D quantitative structure activity relationship（3D-QSAR） model of CoMFA was established with reliable cross-validated correlation coefficient q2 value of 0.585 and Noncross-validated correlation coefficient r2 value of 0.971. This model provided a tool for guiding further design and synthesis of novel pyrrolidine-2,4-dione derivatives with high fungicidal activity.
基金supported by the National Natural Science Foundation of China (21676292,21075138)special fund of State Key Laboratory of Structure Chemistry (2016028)。
文摘A three-dimensional quantitative structure-activity relationship(3 D-QSAR) study was conducted to analyze the A1 AR density(Bmax) of 56 3-aroyl-5-substituted thiophene derivatives(ASTDs) in human A1 Chinese hamster ovary(hA1 CHO) membranes by the comparative molecular field analysis(CoMFA) method. A training set of 45 compounds was used to establish the predictive model, which was verified by the test set of 17 compounds containing template molecule and 5 newly designed molecules. The cross-validation(R2 cv) and non-cross-validation(R2) coefficients of the training set were 0.655 and 0.959, respectively. The model was used to predict the activities of the compounds of the training and test sets, and the results indicated that the models had strong stability and good prediction ability. According to model analysis, the contribution of steric and electrostatic fields was 51.4% and 48.6%, respectively. Based on the 3 D contour maps, five excellent ASTDs agonists were designed, which need to be further verified by biomedical experiments.
基金supported by the National Natural Science Funds of China(21475081)the Natural Science Foundation of Shaanxi Province(2019JM-237)the Graduate Innovation Fund of Shaanxi University of Science and Technology。
文摘Topomer comparative molecular field analysis(Topomer Co MFA)and holographic quantitative structure-activity relationship(HQSAR)for 1302,5-diketopiperazine derivatives were used to build a three-dimensional quantitative structure-activity relationship(3D-QSAR)model.The results show that the models have high predictive ability.For Topomer CoMFA,the cross-validated q^2 value is 0.710 and the non-cross-validated r^2 value is 0.834.The most effective HQSAR model shows that the cross-validation q^2 value is 0.700,the non-cross-validated r^2 value is 0.815,and the best hologram length value is 353 using connections and bonds as fragment distinctions.50 highly active 2,5-diketopiperazine derivatives were designed based on the three-dimensional equipotential map and HQSAR color code map.Finally,the molecular docking method was also used to study the interactions of these new molecules by docking the ligands into the diketopiperazine active site,which revealed the likely bioactive conformations.This study showed that there are extensive interactions between the new molecule and Arg156,Arg122 residues in the active site of diketopiperazine.These results provide useful insights for the design of potent of the new 2,5-diketopiperazine derivatives.
文摘28 kinds of carotenoids are studied to reveal the key parameters and regulation on the singlet oxygen quenching rate.First,the quantum chemistry parameters of carotenoids calculated by Gaussian software combined with substitution parameters were used to construct the quantitative structure-activity relationship model(QSAR)of the singlet oxygen quenching rate of carotenoids.The key parameters affecting the antioxidant activity of carotenoids are revealed,and the data predicted via the QSAR model were provided for subsequent research.Then,a three-dimensional(3D)pharmacophore model was used to regulate and modify the antioxidant activity of carotenoids.The correlation coefficients of the modeling group(R2)and verification group(Rpre2)of the established QSAR model were 0.945 and 0.916,respectively,which can be used for the analysis of antioxidant activity of carotenoids;the antioxidant activity of carotenoids can be significantly regulated by the number of conjugated C=C bonds,the energy difference between frontier molecular orbitals and the partial Mulliken charge in C1 and theπ···π*excitation energy E(s);the antioxidant activity of carotenoids can be effectively regulated by the hydrogen bond acceptor pharmacophores on both sides of the conjugated C=C bonds and the hydrophobic groups on the conjugated C=C bond;the hydrophobic substituents attached to conjugated C=C bonds can effectively improve the singlet oxygen quenching rate of carotenoids.
