An Enhanced Comparative Molecular Field Analysis Method Using Genetic Algorithm

In this study. an automated conformer selection procedure using generic algorithm (GA) has been applied in comparative molecular field analysis (CoMFA) method. Using genetic algorithm. the 3D-QSAR model is optimized to an optimal one. From the calculation results, a group of QSAR models with high predictive ability can be obtained, which is superior than using conventional CoMFA: meanwhile. the active conformers for these compounds in data set can be determined fi om the best model.

Molecular Modeling and Design of Arylthioindole Derivatives as Tubulin Inhibitors

Three-dimensional quantitative structure activity relationship （3D-QSAR） and docking studies of a series of arylthioindole derivatives as tubulin inhibitors against human breast cancer cell line MCF-7 have been carried out. An optimal 3D-QSAR model from the comparative molecular field analysis （CoMFA） for training set with significant statistical quality （R2=0.898） and predictive ability （q2=0.654） was established. The same model was further applied to predict pIC50 values of the compounds in test set, and the resulting predictive correlation coefficient R2（pred） reaches 0.816, further showing that this CoMFA model has high predictive ability. Moreover, the appropriate binding orientations and conformations of these compounds interacting with tubulin are located by docking study, and it is very interesting to find the consistency between the CoMFA field distribution and the 3D topology structure of active site of tubulin. Based on CoMFA along with docking results, some important factors improving the activities of these compounds were discussed in detail and were summarized as follows： the substituents R3-R5 （on the phenyl ring） with higher electronegativity, the substituent R6 with higher eleetropositivity and bigger bulk, the substituent R7 with smaller bulk, and so on. In addition, five new compounds with higher activities have been designed. Such results can offer useful theoretical references for experimental works.

3D-QSAR Study of 7,8-Dialkyl-l,3-diaminopyrrolo-[3,2-f] Quinazolines with Anticancer Activity as DHFR Inhibitors

A three-dimensional quantitative structure-activity relationship （3D-QSAR） study of a series of 7,8-dialkyl-l,3-diaminopyrrolo-[3,2-f] quinazolines with anticancer activity as dihydrofo- late reductase （DHFR） inhibitors was carried out by using the comparative molecular field analysis （CoMFA）, on the basis of our reported 2D-QSAR of these compounds. The es- tablished 3D-QSAR model has good quality of statistics and good prediction ability; the non cross-validation correlation coefficient and the cross-validation value of this model are 0.993 and 0.619, respectively, the F value is 193.4, and the standard deviation SD is 0.208. This model indicates that the steric field factor plays a much more important role than the electrostatic one, in satisfying agreement with the published 2D-QSAR model. However, the 3D-QSAR model offers visual images of the steric field and the electrostatic field. The 3D-QSAR study further suggests the following： to improve the activity, the substituent R^1 should be selected to be a group with an adaptive bulk like Et or i-Pr, and the substituent R should be selected to be a larger alkyl. In particular, based on our present 3D-QSAR as well as the published 2D-QSAR, the experimentMly-proposed hydrophobic binding mechanism on the receptor-binding site of the DHFR can be further explained in theory. Therefore, the QSAR studies help to further understand the ＂hydrophobic binding＂ action mechanism of this kind of compounds, and to direct the molecular design of new drugs with higher activity.

Three-dimensional pharmacophore screening for fentanyl derivatives

Fentanyl is a highly selective u-opioid receptor agonist with high analgesic activity. Three-dimensional pharmacophore models were built from a set of 50 fentanyl derivatives. These were employed to elucidate ligand-receptor interactions using information derived only from the ligand structure to identify new potential lead compounds. The present studies demonstrated that three hydrophobic regions, one positive ionizable region and two hydrogen bond acceptor region sites located on the molecule seem to be essential for analgesic activity. The results of the comparative molecular field analysis model suggested that both steric and electrostatic interactions play important roles. The contributions from steric and electrostatic fields for the model were 0.621 and 0.379, respectively. The pharmacophore model provides crucial information about how well the common features of a subject molecule overlap with the hypothesis model, which is very valuable for designing and optimizing new active structures.

2D-and 3D-QSBR Studies on the Relationship between Structure and Biodegradability of Phthalates

Nine phthalates were calculated at the B3LYP/6-311G＊＊ level using DFT method. The corresponding linear relationship equations （R2 were 0.853 and 0.936 respectively） for the biodegradation rate （Kb） and half-life time （h/2） of biodegradation were obtained with the structural parameters as theoretical descriptors. Furthermore, CoMFA method was also applied to establish 3D models which revealed the fields influencing these properties. The relationship between the properties and the structure was obtained. The correlation coefficients of the models were 0.992 and 0.999, respectively. Analyses of 2D and 3D models demonstrated that the molecular volume was an important factor affecting the biodegradability of these compounds.

Quantitative structure-activity relationship of 2-alkyl-4-(biphenylylmethoxy) pyridine derivatives with AT1 receptor antagonistic activity

The quantitative structure-activity relationship(QSAR) of 2-alkyl-4-(biphenylylmethoxy) pyridine derivatives was studied.Three different alignment methods were used to get the models of the comparative molecular field analysis(CoMFA),the comparative molecular similarity indices analysis(CoMSIA),and the hologram quantitative structure?activity relationship(HQSAR).The statistical results from the established models show believable predictivity based on the cross-validated value(q2>0.5) and the non-validated value(r2>0.9),The analysis on contour maps of CoMFA and CoMSIA models suggests that hydrophobic and hydrogen-bond acceptor fields are important factors that affect the AT1 antagonistic activity of 2-alkyl-4-(biphenylylmethoxy) pyridine derivatives besides the steric and electrostatic fields,The structural modification information from different atom contributions in the HQSAR model is in agreement with that in the 3D-QSAR models.

QSPR Studies on the Octanol/water Partition Coefficient (lgK_(ow)) of Substituted Anilines with 2D and 3D Methods

Octanol/water partition coefficient （Kow） is a crucial property for evaluating the environmental behavior and fate of organic compound. Herein, some quantitative structure-property relationship （QSPR） studies were performed to estimate and predict the lgK ow of substituted anilines. 2D method （multiple linear regression, MLR） and 3D method （comparative molecular field analysis, CoMFA） were applied in this study. Successful 2D and 3D models yielded the correlation coefficient （R2） values of 0.981 and 0.966 and the Leave-One-Out （LOO） cross-validated correlation coefficient （q2） values of 0.933 and 0.820, respectively. The developed models have a highly predictive ability in both internal and external validation. In addition, the results were interpreted in terms of physical and chemical meanings of descriptors and field contribution maps. It showed that the steric and electrostatic properties are the primary factors that govern the lgK ow of substituted anilines. The information obtained from the QSPR models would be helpful to the interpretation of structural features pertinent to the lgK ow of substituted anilines, which may be helpful in estimating the organic compounds＇ potential harm to the environment.

CoMFA Model of Anti-tumor Activity for Fluoroquinolon-3-yl s-Triazole Sulfide-ketone Derivatives and Implications for Molecular Design

Comparative molecular field analysis(CoMFA)techniques were used to perform three-dimensional quantitative structure-activity relationship(3D-QSAR)studies on the anti-tumor activity(pIH and pIC)of 28 fluoroquinolon-3-yl s-triazole sulfide-ketone derivatives(FQTSDs)against two cancer cell lines,including human hepatoma Hep-3B cells and human pancreatic cancer Capan-1 cells.23 compounds were randomly selected as the training set to establish the prediction models,which were verified by the test set of 6 compounds containing template molecule.The obtained cross-validation(Rcv2)and non-cross-validation correlation coefficients(R2)of the CoMFA models were 0.477 and 0.850 for pIH,and 0.421 and 0.836 for pIC,respectively.The contributions of steric and electrostatic fields to pIH were determined to be 48.1%and 51.9%,and those to pIC were 49.4%and 50.6%,respectively.The CoMFA models were then used to predict the activities of the compounds in the training and testing sets,and the models had a strong stability and good predictability.Based on the 3D contour maps,four novel FQTSDs with a higher anti-tumor activity were designed.However,the effectiveness of these novel FQTSDs is still needed to be verified by experimental results.

CoMFA Model and Molecular Design of Anti-excitatory Activity for Benzodiazepinooxazole Derivatives against Mice

A 3D-QSAR study was conducted to analyze the anti-excitatory activity(p E)of benzodiazepinooxazole derivatives to mice by the comparative molecular field analysis(CoMFA)method.Among the 54 active molecules,a training set of 46 compounds was randomly selected to construct the CoMFA model;the remaining compounds,together with template molecule(No.54)and two newly designed molecules constitute a test set of 17 compounds to validate the model.The obtained cross-validation coefficient(R_(cv)^(2)),the non-cross validation coefficient(R^(2)),and the test value F of the CoMFA model for training set are 0.516,0.899,and 57.57,respectively.The model was used to predict the activities of all compounds in the training and testing sets,and the results indicated that the model had good correlation,strong stability and good predictability.Based on the 3D contour maps,eight novel benzodiazepinooxazole derivatives with higher anti-excitatory activity were designed.However,the effectiveness of these novel benzodiazepinooxazole derivatives is still needed to be verified by the experimental results.

Construction of the Molecular Structure Model of the Zhaotong Lignite Using Simulation and Experiment Data

Aiming to better understand the physiochemical properties of lignite, we select Zhaotong lignite as object and adopt simulation and experiment data to construct its molecular structure. Firstly, the important parameters including carbon skeleton, valence state and functional group of the sample are obtained by ultimate analysis, 13 C NMR, XPS and Py-GC/MS. Results indicate that the ratio of aromatic carbon and aromatic bridge carbon to surrounding carbon of the sample are 40.32% and 0.14, respectively. Such results imply that the aromatic structure of the sample is dominated by benzene and naphthalene. Moreover, the ratio of aliphatic carbon is 51.55%, and the aliphatic structure is mainly comprised by methyl, methylene, quaternary carbon and oxygen-aliphatic carbon. Oxygen atoms principally exist in ether, carbonyl and carboxyl groups, of which ether accounts for 70.2%. Additionally, the contents of pyridine, pyrrole and quaternary nitrogen are 25.2%, 46.3% and 13.0%, respectively. Based on the aforementioned results, the molecular structure model of Zhaotong lignite is constructed by the method of computer-aided molecular design. Subsequently, the molecular formula of Zhaotong lignite is calculated as C;H;O;N;. Finally, in order to verify the reasonability of the constructed model, the 13 C NMR of the molecular structure model is simulated by employing the basis set of GIAO/6-31G at the Gaussian 09 computing platform. These simulated results agree well with the experimental ones, which suggests that the molecular structure model of Zhaotong lignite is accurate and reasonable.

3D-QSAR Models of Anti-tumor Activity for Histone Deacetylase Inhibitors Containing Dihydropyridin-2-one

A 3D-QSAR study was conducted to analyze the anti-tumor activity(pHs,s=1,6)of dihydropyridin-2-one containing histone deacetylase inhibitor(DHDACi)to histone deacetylase(HDACs,s=1,6)by the comparative molecular field analysis(CoMFA)method.The predicting model was established based on the training set of 22 compounds,which was verified by the test set of 6 compounds containing template molecule.The results showed that the contributions of steric and electrostatic fields to pH1 are 37.6%and 62.4%,and those to pH6 are 44.6%and 55.4%,respectively.The coefficients of the cross-validation(Rcv2)and the non cross-validation(R2)are 0.574 and 0.947 for pH1,and 0.488 and 0.884 for pH6,respectively.The models were then used to predict the activities of the compounds for the training and testing sets.The results indicated that the models had strong stability and good predictability.Based on the 3D contour maps,several new potential inhibitors with higher anti-tumor activity were designed.However,the effectiveness of these potential inhibitors is still needed to be verified by the experimental results.

Quantitative structure-activity relationships of antimicrobial fatty acids and derivatives against Staphylococcus aureus

Fatty acids and derivatives(FADs)are resources for natural antimicrobials.In order to screen for additional potent antimicrobial agents,the antimicrobial activities of FADs against Staphylococcus aureus were examined using a microplate assay.Monoglycerides of fatty acids were the most potent class of fatty acids,among which monotridecanoin possessed the most potent antimicrobial activity.The conventional quantitative structure-activity relationship(QSAR)and comparative molecular field analysis(CoMFA)were performed to establish two statistically reliable models(conventional QSAR:R2=0.942,Q 2 LOO=0.910;CoMFA:R 2=0.979,Q 2=0.588,respectively).Improved forecasting can be achieved by the combination of these two models that provide a good insight into the structureactivity relationships of the FADs and that may be useful to design new FADs as antimicrobial agents.

Isosteric design of friction-reduction and anti-wear lubricant additives with less sulfur content

To reduce harmful sulfur content in lubricant additives, making use of isosterism has been shown to be an effective strategy. When thiobenzothiazole compounds were used as templates, the exchange of sulfur atoms in the thiazole ring with oxygen atoms and NH groups produced twelve isosteres. Similarly, 2-benzothiazole- S-carboxylic acid esters were used as template molecules to produce six isosteres. About 30% of the isosteres exhibited a satisfactory deviation of ±5% relative to the template, ignoring the specific changes in the base oils, the differences in molecular structure, and the friction or wear properties. The template molecules and isosteres in triisodecyl trimellitate exhibited better tribological properties than in trimethylolpropane trioleate or bis(2- ethylhexyl) adipate. Comparative molecular field analysis(CoM FA)- and comparative molecular similarity index analysis(CoMSIA)-quantitative structure tribo-ability relationship(QSTR) models were employed to study the correlation of molecular structures between the base oils and additives. The models indicate that the higher the structural similarities of the base oils and additives are, the more synergetic the molecular force fields of the lubricating system are; the molecular force fields creating synergistic effects will improve tribological performance.

CoMFA Study on Anti-proliferative Activity of Fluoroquinolone Amide Derivatives

The in vitro anti-proliferative activity(pICi,i=hp,ca,hl)of fluoroquinolone(rhodanineα,β-unsaturated ketone)amide compounds,referred to as“fluoroquinolone amide derivatives(FQADs)”towards Hep-3B,Capan-1 and HL60 cells,was studied by the 3D-QSAR method of comparative molecular field analysis(CoMFA).Based on the training set of 14 compounds,the prediction model was established,which was further verified by the test set of 5 compounds with template molecule included.It is found that steric and electrostatic fields contribute 66.8%and 33.2%to pIChp,61.4%and 38.6%to pICca,and 61.5%and 38.5%to pIChl,respectively.The Rcv 2(i.e,cross-validation coefficient)is 0.324,0.381,and 0.421 for pIChp,pICca,and pIChl,respectively,while the corresponding R2(i.e,non-cross-validation coefficient)all reach 0.999.Then,the models were employed to estimate the activities of the training and test compounds,and the results show that the stability and predictability of developed models are very satisfactory.According to the contour maps of steric and electronic fields,bulky groups linked to 2-,3-,4-positions of phenyl ring,and electropositive groups near the 4-position and electronegative groups far away may increase the anti-proliferative activity.Using the information provided by the 3D contour maps,four new FQADs owing higher antiproliferative activity were designed,but their effectiveness should be further tested by experiments.

Study on the Biological Activity of 3-Aroyl-5-substituted Thiophene Derivatives Based on the CoMFA Method

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.

Pharmacophore Screening on Piperidinecarboxamides Derivatives Based on GALAHAD and CoMFA Models

In order to discover the novel anticonvulsant drugs, pharmacophore screening of the anticonvulsant inhibitors was enforced. Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets （GALAHAD） and Comparative Molecular Field Analysis （CoMFA） studies were combined to implement our research. Firstly, multiple models were generated using GALAHAG based on high active molecules. Secondly, several of them were validated using the CoMFA study. Finally, a good values of q2 from training set and promising predictive power from test set were obtained based on one model simutaneously. One model had been selected as the most reasonable pharmacophore model. The results of the CoMFA study based on the model 1 suggested that both steric and electrostatic interactions played important roles.

Study on the Three-dimensional Quantitative Structure-activity Relationship of Pyridazinonyl-substituted 1,3,4-Thiadiazoles

The three-dimensional quantitative structure-activity relationships of a series of 5-[ 1-aryl-1,4-dihydro-6-methylpyridazin-4-one-3-yl]-2-arylamino-1,3,4-thiadiazoles, related to the fungicidal activity, were studied using the comparative molecular field analysis （CoMFA）. The results show that the contributions of steric and electrostatic fields to the activity are 0.505 and 0.495, respectively. The cross-validated q^2 and the correlation coefficient r^2 for the model established by the study are 0.769 and 0.938, respectively, with the F value of 60.996, and the standard deviation s of 0.074. These values indicate that the model is significant and has good predictability. The analysis results are in good agreement well with the study of 2D-QSAR, and offered important structural insights into designing highly active compounds prior to synthesis.

3D-QSAR Studies on the Imidazopyrimidine Derivatives

Comparative molecular field analysis(CoMFA) and comparative molecular similarity indices analysis(CoMSIA) for imidazopyrimidine derivatives were performed to get the molecular active conformation selection, molecular alignment, as well as the establishment of corresponding 3 D-QSAR model. The model established by this method has good ability to predict such compounds. For CoMFA model, the cross-validated q2 and non-cross-validated r2 values are 0.665 and 0.872, respectively. The best q2 value for CoMSIA model is 0.632 and r2 value is 0.923. Using this information and the three-dimensional equipotential map for molecular design can theoretically obtain some new antibacterial drugs with higher activity. There are two newly designed molecules with activity values of 7.921 and 7.872, which are higher than that of the template molecule No. 12 with an activity value of 7.850, and the QSAR research results can provide a theoretical reference for the synthesis of new drugs.