3D QSAR studies of 1,3,4-benzotriazepine derivatives as CCK2 receptor antagonists

A number of CCK(2) antagonists have been reported to play an important role in controlling gastric acid-related conditions, nervous system related disorders and certain types of cancer. To obtain the helpful information for designing potent antagonists with novel structures and to investigate the quantitative structure-activity relationship of a group of 62 different CCK(2) receptor antagonists with varying structures and potencies, CoMFA, CoMSIA, and HQSAR studies were carried out on a series of 1,3,4-benzotriazepine-based CCK(2) receptor antagonists. QSAR models were derived from a training set of 49 compounds. By applying leave-one-out (LOO) cross-validation study, cross-validated (r(cv)(2)) values of 0.673 and 0.608 and non-cross-validated (r(ncv)(2)) values of 0.966 and 0.969 were obtained for the CoMFA and CoMSIA models, respectively. The predictive ability of the CoMFA and CoMSIA models was determined using a test set of 13 compounds, which gave predictive correlation coefficients (r(pred)(2)) of 0.793 and 0.786, respectively. HQSAR was also carried out as a complementary study, and the best HQSAR model was generated using atoms, bonds, hydrogen atoms, and chirality as fragment distinction with fragment size (2-5) and six components showing r(cv)(2) and r(ncv)(2) values of 0.744 and 0.918, respectively. CoMFA steric and electrostatic, CoMSIA hydrophobic and hydrogen bond acceptor fields, and HQSAR atomic contribution maps were used to analyze the structural features of the datasets that govern their antagonistic potency.     

CoMFA methodology in structure-activity analysis of hexahydro- and octahydropyrido[1,2-c]pyrimidine derivatives based on affinity towards 5-HT1A, 5-HT2A and alpha1-adrenergic receptors

Structural features of the pyrido[1,2-c]pyrimidine derivatives with arylpiperazine moiety and their affinities towards 5-HT1A, 5-HT2A and alpha1-adrenergic receptors were analyzed using the CoMFA procedure. On the basis of 3D-QSAR models for the 5-HT2A and alpha1-adrenergic receptors, four compounds with expected better affinity/selectivity were proposed and synthesized. The affinities obtained confirm experimentally the usefulness of CoMFA models. Our results suggest that active conformations adopted by the studied molecules when interacting with the receptors are neutral instead of the protonated ones.     

3D QSAR studies on a series of potent and high selective inhibitors for three kinases of RTK family

For targets belonging to the same family of receptors, inhibitors often act at more than one biological target and produce a synergistic effect. Separate CoMFA and CoMSIA models were developed from our data set for the KDR, cKit and Tie-2 inhibitors. These models showed excellent internal predictability and consistency, and validation using test-set compounds yielded a good predictive power for the pIC(50) value. The field contour maps (CoMFA and CoMSIA) corresponding to the KDR, cKit and Tie-2 kinase subtypes reflected the characteristic similarities and differences between these types. These maps provided valuable information to facilitate structural modifications of the inhibitor to increase selectivity for the KDR over cKit and Tie-2.     

An investigation of structurally diverse carbamates for acetylcholinesterase (AChE) inhibition using 3D-QSAR analysis

In order to identify the essential structural features and physicochemical properties for acetylcholinesterase (AChE) inhibitory activity in some carbamate derivatives, the systematic QSAR (Quantitative Structure Activity Relationship) studies (CoMFA, advance CoMFA and CoMSIA) have been carried out on a series of (total 78 molecules) taking 52 and 26 molecules in training and test set, respectively. Statistically significant 3D-QSAR (three-dimensional Quantitative Structure Activity Relationship) models were developed on training set molecules using CoMFA and CoMSIA and validated against test set compounds. The highly predictive models (CoMFA q(2)=0.733, r(2)=0.967, predictive r(2)=0.732, CoMSIA q(2)=0.641, r(2)=0.936, predictive r(2)=0.812) well explained the variance in binding affinities both for the training and the test set compounds. The generated models suggest that steric, electrostatic and hydrophobic interactions play an important role in describing the variation in binding affinity. In particular the carbamoyl nitrogen should be more electropositive; substitutions on this nitrogen should have high steric bulk and hydrophobicity while the amino nitrogen should be electronegative in order to have better activity. These studies may provide important insights into structural variations leading to the development of novel AChE inhibitors which may be useful in the development of novel molecules for the treatment of Alzheimer's disease.     

Structural and chemical basis for enhanced affinity and potency for a large series of estrogen receptor ligands: 2D and 3D QSAR studies

The estrogen receptor (ER) is an important drug target for the development of novel therapeutic agents for the treatment of breast cancer. Progress towards the design of more potent and selective ER modulators requires the optimization of multiple ligand-receptor interactions. Comparative molecular field analyses (CoMFA) and hologram quantitative structure-activity relationships (HQSAR) were conducted on a large set of ERalpha modulators. Two training sets containing either 127 or 69 compounds were used to generate QSAR models for in vitro binding affinity and potency, respectively. Significant correlation coefficients (affinity models, CoMFA, r(2)=0.93 and q(2)=0.79; HQSAR, r(2)=0.92 and q(2)=0.71; potency models, CoMFA, r(2)=0.94 and q(2)=0.72; HQSAR, r(2)=0.92 and q(2)=0.74) were obtained, indicating the potential of the models for untested compounds. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. The final QSAR models as well as the information gathered from 3D contour maps should be useful for the design of novel ERalpha modulators having improved affinity and potency.     

3D-QSAR and molecular docking studies of 1,3,5-triazene-2,4-diamine derivatives against r-RNA: novel bacterial translation inhibitors

Aminoglycoside mimetics inhibit bacterial translation by interfering with the ribosomal decoding site. To elucidate the structural properties of these compounds important for antibacterial activity, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to a set of 56 aminoglycosides mimetics. The successful CoMFA model yielded the leave-one-out (LOO) cross-validated correlation coefficient (q(2)) of 0.708 and a non-cross-validated correlation coefficient (r(2)) of 0.967. CoMSIA model gave q(2)=0.556 and r(2)=0.935. The CoMFA and CoMSIA models were validated with 36 test set compounds and showed a good r(pred)(2) of 0.624 and 0.640, respectively. Contour maps of the two QSAR approaches show that electronic effects dominantly determine the binding affinities. These obtained results were agreed well with the experimental observations and docking studies. The results not only lead to a better understanding of structural requirements of bacterial translation inhibitors but also can help in the design of novel bacterial translation inhibitors.     

3D-QSAR and molecular docking studies of selective agonists for the thyroid hormone receptor beta

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed using comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) on a series of agonists of thyroid hormone receptor beta (TRbeta), which may lead to safe therapies for non-thyroid disorders while avoiding the cardiac side effects. The reasonable q(2) (cross-validated) values 0.600 and 0.616 and non-cross-validated r(2) values of 0.974 and 0.974 were obtained for CoMFA and CoMSIA models for the training set compounds, respectively. The predictive ability of two models was validated using a test set of 12 molecules which gave predictive correlation coefficients (r(pred)(2)) of 0.688 and 0.674, respectively. The Lamarckian Genetic Algorithm (LGA) of AutoDock 4.0 was employed to explore the binding mode of the compound at the active site of TRbeta. The results not only lead to a better understanding of interactions between these agonists and the thyroid hormone receptor beta but also can provide us some useful information about the influence of structures on the activity which will be very useful for designing some new agonist with desired activity.     

Structural investigation of PAP derivatives by CoMFA and CoMSIA reveals novel insight towards inhibition of Bcr-Abl oncoprotein

Molecular modeling by 3D-QSAR comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were employed on a series of phenylaminopyrimidine-based (PAP) Bcr-Abl inhibitors. The chemical structures of 63 PAP analogues were aligned using a template extracted from the crystal structure of STI571 bound to Abl kinase. Subsequently, the structures built were divided into training and test sets that include 53 and 10 compounds, respectively. Statistical results showed that the 3D-QSAR models generated from CoMSIA were superior to CoMFA (CoMSIA; q2=0.66, r2=0.94, N=3, F=139.09, r2pred=0.64 while CoMFA; q2=0.53, r2=0.73, N=3, F=43.53, r2pred=0.61). Based on the contour interpretation, the attachment of hydrophobic and bulky groups to the phenyl and pyrrolidine (D- and E-ring of NS-187, respectively) along with highly electronegative groups around the D-ring are important structural features for the design of second-generation Bcr-Abl inhibitors. The generated models are predictive based on reproducible values of the predicted compared with experimental activities in the test set. Further, the complementary analysis of contour maps to the Bcr-Abl binding site suggested the anchor points for binding affinity.     

Insight into the structural requirements of proton pump inhibitors based on CoMFA and CoMSIA studies

In the present study, a series of 179 quinoline and quinazoline heterocyclic analogues exhibiting inhibitory activity against Gastric (H+/K+)-ATPase were investigated using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA) methods. Both the models exhibited good correlation between the calculated 3D-QSAR fields and the observed biological activity for the respective training set compounds. The most optimal CoMFA and CoMSIA models yielded significant leave-one-out cross-validation coefficient, q(2) of 0.777, 0.744 and conventional cross-validation coefficient, r(2) of 0.927, 0.914 respectively. The predictive ability of generated models was tested on a set of 52 compounds having broad range of activity. CoMFA and CoMSIA yielded predicted activities for test set compounds with r(pred)(2) of 0.893 and 0.917 respectively. These validation tests not only revealed the robustness of the models but also demonstrated that for our models r(pred)(2) based on the mean activity of test set compounds can accurately estimate external predictivity. The factors affecting activity were analyzed carefully according to standard coefficient contour maps of steric, electrostatic, hydrophobic, acceptor and donor fields derived from the CoMFA and CoMSIA. These contour plots identified several key features which explain the wide range of activities. The results obtained from models offer important structural insight into designing novel peptic-ulcer inhibitors prior to their synthesis.     

3D-QSAR and molecular docking studies on pyrazolopyrimidine derivatives as glycogen synthase kinase-3beta inhibitors

Glycogen synthase kinase-3 (GSK-3), a serine/threonine kinase, is a fascinating enzyme with diverse biological actions in intracellular signaling systems, making it an emerging target for diseases such as diabetes mellitus, cancer, chronic inflammation, bipolar disorders and Alzheimer's disease. It is important to inhibit GSK-3 selectively and the net effect of the GSK-3 inhibitors thus should be target specific, over other phylogenetically related kinases such as CDK-2. In the present work, we have carried out three-dimensional quantitative structure activity relationship (3D-QSAR) studies on novel class of pyrazolopyrimidine derivatives as GSK-3 inhibitors reported to have improved cellular activity. Docked conformation of the most active molecule in the series, which shows desirable interactions in the receptor, was taken as template for alignment of the molecules. Statistically significant CoMFA and CoMSIA models were generated using 49 molecules in training set. By applying leave-one-out (LOO) cross-validation study, r(cv)2 values of 0.53 and 0.48 for CoMFA and CoMSIA, respectively and non-cross-validated (r(ncv)2) values of 0.98 and 0.92 were obtained for CoMFA and CoMSIA models, respectively. The predictive ability of CoMFA and CoMSIA models was determined using a test set of 12 molecules which gave predictive correlation coefficients (r(pred)2) of 0.47 and 0.48, respectively, indicating good predictive power. Based upon the information derived from CoMFA and CoMSIA contour maps, we have identified some key features that explain the observed variance in the activity and have been used to design new pyrazolopyrimidine derivatives. The designed molecules showed better binding affinity in terms of estimated docking scores with respect to the already reported systems; hence suggesting that newly designed molecules can be more potent and selective towards GSK-3beta inhibition.     

Application of interval type-2 fuzzy neural networks in non-linear identification and time series prediction

Neural networks (NNs), type-1 fuzzy logic systems and interval type-2 fuzzy logic systems (IT2FLSs) have been shown to be important methods in real world applications, which range from pattern recognition, time series prediction, to intelligent control. Recent research shows that embedding an IT2FLS on an NN can be very effective for a wide number of non-linear complex systems, especially when handling imperfect or incomplete information. In this paper we are presenting several models of interval type-2 fuzzy neural networks (IT2FNNs) that use a set of rules and interval type-2 membership functions for that purpose. Simulation results of non-linear function identification using the IT2FNN for one and three variables and for the Mackey–Glass chaotic time series prediction are presented to illustrate that the proposed models have potential for real world applications.     

A multi-objective optimization of type-2 fuzzy control speed in FPGAs

This paper proposes a design of multi-objective genetic optimization for the average approximation of an interval type-2 fuzzy logic controller (AT2-FLC) using linear combination of individual criteria. There has been shown, on the real case, that the proposed method can be competitive to other commonly used approaches in the design of fuzzy controllers. The AT2-FLC was tested with different levels of uncertainty and different number of bits for the VHDL codification to regulate speed in a direct current motor (ReSDCM). Comparisons were made between the type-1 fuzzy logic controller versus AT2-FLC synthesized in VHDL code for FPGA and the AT2-FLC in VHDL versus the PID controller to ReSDCM. The main contribution of the paper is the design, implementation and comparison of multi-objective GA optimization of AT2-FLC for FPGA real applications. The AT2-FLC is targeted to a Xilinx Spartan 3A XC3S700A device using the Xilinx Foundation Environment.     

A type-2 neural fuzzy system learned through type-1 fuzzy rules and its FPGA-based hardware implementation

This paper first proposes a type-2 neural fuzzy system (NFS) learned through its type-1 counterpart (T2NFS-T1) and then implements the built IT2NFS-T1 in a field-programmable gate array (FPGA) chip. The antecedent part of each fuzzy rule in the T2NFS-T1 uses interval type-2 fuzzy sets, while the consequent part uses a Takagi-Sugeno-Kang (TSK) type with interval combination weights. The T2NFS-T1 uses a simplified type-reduction operation to reduce system training time and hardware implementation cost. Given a training data set, a TSK type-1 NFS is first learned through structure and parameter learning. The built type-1 fuzzy logic system (FLS) is then extended to a type-2 FLS, where highly overlapped type-1 fuzzy sets are merged into interval type-2 fuzzy sets to reduce the total number of fuzzy sets. Finally, the rule consequent and antecedent parameters in the T2NFS-T1 are tuned using a hybrid of the gradient descent and rule-ordered recursive least square (RLS) algorithms. Simulation results and comparisons with various type-1 and type-2 FLSs verify the effectiveness and efficiency of the T2NFS-T1 for system modeling and prediction problems. A new hardware circuit using both parallel-processing and pipeline techniques is proposed to implement the learned T2NFS-T1 in an FPGA chip. The T2NFS-T1 chip reduces the hardware implementation cost in comparison to other type-2 fuzzy chips.     

CoMFA analysis on a set of new noncompetitive GABAA receptor antagonists： fipronil and related analogs

Fipronil and related analogs, a set of new noncompetitive GABAA receptor antagonists, were investigated using comparative molecular field analysis （CoMFA） to explore their three-dimensional quantitative structure-activity relationships （3D-QSAR）. Considering the structural complexity of molecules of fipronil and related analogs, three different alignments were performed in this paper. CoMFA model for housefly receptor yield the leave-one-out and cross-validated correlation coefficient q^2 value of 0.511 and the conventional correlation coefficient r^2 value of 0.997. The new compounds with higher activity would be designed from this model. CoMFA model for rat receptor was not successful using all these three alignments, the reason of which maybe that some molecules adopt different conformations for rat receptor.     

两类促肾上腺皮质释放因子(CRF)抑制剂的CoMFA研究

Fipronil and related analogs, a set of new noncompetitive GABAA receptor antagonists, were investigated using comparative molecular field analysis (CoMFA) to explore their three-dimensional quantitative structure-activity relationships (3D-QSAR).Considering the structural complexity of molecules of fipronil and related analogs, three different alignments were performed in this paper. CoMFA model for housefly receptor yield the leave-one-out and cross-validated correlation coefficient q2 value of 0.511 and the conventional correlation coefficient r2 value of 0.997. The new compounds with higher activity would be designed from this model.CoMFA model for rat receptor was not successful using all these three alignments, the reason of which maybe that some molecules adopt different conformations for rat receptor.     

The collapsing method of defuzzification for discretised interval type-2 fuzzy sets

This paper proposes a new approach for defuzzification of interval type-2 fuzzy sets. The collapsing method converts an interval type-2 fuzzy set into a type-1 representative embedded set (RES), whose defuzzified values closely approximates that of the type-2 set. As a type-1 set, the RES can then be defuzzified straightforwardly. The novel representative embedded set approximation (RESA), to which the method is inextricably linked, is expounded, stated and proved within this paper. It is presented in two forms: Simple RESA: this approximation deals with the most simple interval FOU, in which a vertical slice is discretised into 2 points. Interval RESA: this approximation concerns the case in which a vertical slice is discretised into 2 or more points. The collapsing method (simple RESA version) was tested for accuracy and speed, with excellent results on both criteria. The collapsing method proved more accurate than the Karnik-Mendel iterative procedure (KMIP) for an asymmetric test set. For both a symmetric and an asymmetric test set, the collapsing method outperformed the KMIP in relation to speed.     

双环硫化磷酸酯类化合物的三维定量构效关系研究

为获取双环硫化磷酸酯类化合物对昆虫γ-氨基丁酸(GABA)受体和哺乳动物γ-氨基丁酸受体的亲合选择性定量信息,基于实验所测定的双环硫化磷酸酯类化合物与家蝇及大白鼠GABA受体结合的相对活性数据,以比较分子场分析法进行了三维定量构效关系研究。结果表明,家蝇GABA受体的亲合区域有足够的空间容纳异丙基和异丁基,但大白鼠GABA受体的亲合区域不具有这样的空间。     

Experimental study of intelligent controllers under uncertainty using type-1 and type-2 fuzzy logic

Uncertainty is an inherent part in control systems used in real world applications. The use of new methods for handling incomplete information is of fundamental importance. Type-1 fuzzy sets used in conventional fuzzy systems cannot fully handle the uncertainties present in control systems. Type-2 fuzzy sets that are used in type-2 fuzzy systems can handle such uncertainties in a better way because they provide us with more parameters and more design degrees of freedom. This paper deals with the design of control systems using type-2 fuzzy logic for minimizing the effects of uncertainty produced by the instrumentation elements, environmental noise, etc. The experimental results are divided in two classes, in the first class, simulations of a feedback control system for a non-linear plant using type-1 and type-2 fuzzy logic controllers are presented; a comparative analysis of the systems’ response in both cases was performed, with and without the presence of uncertainty. For the second class, a non-linear identification problem for time-series prediction is presented. Based on the experimental results the conclusion is that the best results are obtained using type-2 fuzzy systems.