Development of docking-based 3D QSAR models for the design of substituted quinoline derivatives as human dihydroorotate dehydrogenase (hDHODH) inhibitors

Abstract

This study has investigated docking-based 3D quantitative structure–activity relationships (QSARs) for a range of quinoline carboxylic acid derivatives by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). A docking study has shown that most of the compounds formed H-bonds with Arg136 and Gln47, which have already been shown to be essential for the binding of ligands at the active site of the hydroorotate dehydrogenase adenovirus (hDHODH). Bioactive conformations of all the molecules obtained from the docking study were used for the 3D QSAR study. The best CoMFA and CoMSIA models were obtained for the training set and were found to be statistically significant, with cross-validated coefficients (q² ) of 0.672 and 0.613, r² _cv of 0.635 and 0.598 and coefficients of determination (r² ) of 0.963 and 0.896, respectively. Both models were validated by a test set of 15 compounds, giving satisfactory predicted correlation coefficients (r² _pred) of 0.824 and 0.793 for the CoMFA and CoMSIA models, respectively. From the docking-based 3D QSAR study we designed 34 novel quinoline-based compounds and performed structure-based virtual screening. Finally, in silico pharmacokinetics and toxicities were predicted for 24 of the best docked molecules. The study provides valuable information for the understanding of interactions between hDHODH and the novel compounds.     

Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) using comparative molecular field analysis (CoMFA) was performed on a series of substituted tetrahydropyran (THP) derivatives possessing serotonin (SERT) and norepinephrine (NET) transporter inhibitory activities. The study aimed to rationalize the potency of these inhibitors for SERT and NET as well as the observed selectivity differences for NET over SERT. The dataset consisted of 29 molecules, of which 23 molecules were used as the training set for deriving CoMFA models for SERT and NET uptake inhibitory activities. Superimpositions were performed using atom-based fitting and 3-point pharmacophore-based alignment. Two charge calculation methods, Gasteiger-Hückel and semiempirical PM3, were tried. Both alignment methods were analyzed in terms of their predictive abilities and produced comparable results with high internal and external predictivities. The models obtained using the 3-point pharmacophore-based alignment outperformed the models with atom-based fitting in terms of relevant statistics and interpretability of the generated contour maps. Steric fields dominated electrostatic fields in terms of contribution. The selectivity analysis (NET over SERT), though yielded models with good internal predictivity, showed very poor external test set predictions. The analysis was repeated with 24 molecules after systematically excluding so-called outliers (5 out of 29) from the model derivation process. The resulting CoMFA model using the atom-based fitting exhibited good statistics and was able to explain most of the selectivity (NET over SERT)-discriminating factors. The presence of −OH substituent on the THP ring was found to be one of the most important factors governing the NET selectivity over SERT. Thus, a 4-point NET-selective pharmacophore, after introducing this newly found H-bond donor/acceptor feature in addition to the initial 3-point pharmacophore, was proposed.     

Insight into the structural requirements of benzimidazole derivatives as interleukin‐2 inducible t‐cell kinase inhibitors by computational explorations

In the present work, a set of ligand‐ and receptor‐based 3D‐QSAR models were developed to explore the structure–activity relationship of 109 benzimidazole‐based interleukin‐2‐inducible T‐cell kinase (ITK) inhibitors. In order to reveal the requisite 3D structural features impacting the biological activities, a variety of in silico modeling approaches including the comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), docking, and molecular dynamics were applied. The results showed that the ligand‐based CoMFA model (Q² = 0.552, R²_ncv = 0.908, R²_pred = 0.787, SEE = 0.252, SEP = 0.558) and CoMSIA model (Q² = 0.579, R²_ncv = 0.914, R²_pred = 0.893, SEE = 0.240, SEP = 0.538) were superior to other models with greater predictive power. In addition, a combined analysis between the 3D contour maps and docking results showed that: (1) Compounds with bulky or hydrophobic substituents near ring D and electropositive or hydrogen acceptor groups around rings C and D could increase the activity. (2) The key amino acids impacting the receptor–ligand interactions in the binding pocket are Met438, Asp500, Lys391, and Glu439. The results obtained from this work may provide helpful guidelines in design of novel benzimidazole analogs as inhibitors of ITK. © 2013 Wiley Periodicals, Inc.     

Conceptual DFT properties‐based 3D QSAR: Analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme

Structure‐activity relationships of 46 P450 2A6 inhibitors were analyzed using the 3D‐QSAR methodology. The analysis was carried out to confront the use of traditional steric and electrostatic fields with that of a number of fields reflecting conceptual DFT properties: electron density, HOMO, LUMO, and Fukui f⁻ function as 3D fields. The most predictive models were obtained by combining the information of the electron density with the Fukui f⁻ function (r² = 0.82, q² = 0.72), yielding a statistically significant and predictive model. The generated model was able to predict the inhibition potencies of an external test set of five chemicals. The result of the analysis indicates that conceptual DFT‐based molecular fields can be useful as 3D QSAR molecular interaction fields. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

A facile synthesis of novel 5‐substituted pyridine 2 carboxamide derivatives and their biological evaluation and 3D QSAR studies

A variety of novel 5‐substituted pyridine 2 carboxamides were designed and synthesized using both normal and solvent‐free microwave (MW) irradiation techniques. The results revealed that MW protocol proceeded smoothly under mild reaction conditions in short reaction times, thus avoiding the use of toxic organic solvents. Structural elucidation of the synthesized compounds was carried out on the basis of various spectroscopic methods, such as ¹H NMR, ¹³C NMR, LCMS, and IR. The synthesized compounds were evaluated for their in vitro antimicrobial activity (MIC) using the agar disk diffusion method. Among the various synthetic compounds, compound 3b showed higher potential activity against Escherichia coli than the other compounds. The order of activity against E. coli of the studied compounds is 3b > 3e > 3g > 3h > 3d > 3c > 3a > 3f . Additionally, 2D and 3D structural features of the synthesized derivatives were recognized by the 3D‐QSAR model. This validated model exhibited good internal (r², 0.924) and external prediction (r²pred, 0.851) correlation. The results of QSAR studies concluded that Alog P, the number of hydrogen bond acceptors, and the number of rotatable bonds were necessary features for the activity of the pyridine carboxamide derivatives.     

Design and synthesis of 2-alkylbenzimidazole derivatives as novel non-peptide angiotensin Ⅱ AT1 receptor antagonists

A series of 2-alkylbenzimidazole derivatives 9a-n have been designed and synthesized as a novel class of non-peptide angiotensin Ⅱ AT1 receptor antagonists. The synthesized compounds were evaluated for their antagonism of angiotensin Ⅱ, induced contraction in the rabbit thoracic aortic ring and the results showed that compounds 9a, 9g and 9j exhibited potent antagonistic activity of AT1 receptor.     

光系统Ⅱ抑制剂: 顺式氰基丙烯酸酯化合物的 三维构效关系的电子结构研究

以距离比较法所获得的顺式氰基丙烯酸酯化合物的活性构象为模板,对39个该类化合物采用比较分子场方法进行了三维构效关系的研究。结果表明,所获得的药效团模型具有很好的预测能力。同时采用量子化学的方法对活性构象模板分子电子结构作了讨论。     

Theoretical studies on QSAR and mechanism of 2‐indolinone derivatives as tubulin inhibitors

The theoretical studies on three‐dimensional quantitative structure activity relationship (3D‐QSAR) and action mechanism of a series of 2‐indolinone derivatives as tubulin inhibitors against human breast cancer cell line MDA‐MB‐231 have been carried out. The established 3D‐QSAR model from the comparative molecular field analysis (CoMFA) shows not only significant statistical quality but also predictive ability, with high correlation coefficient (R² = 0.986) and cross‐validation coefficient (q² = 0.683). In particular, the appropriate binding orientations and conformations of these 2‐indolinone derivatives interacting with tubulin are located by docking study, and it is very interesting to find that the plot of the energy scores of these compounds in DOCK versus the corresponding experimental pIC₅₀ values exhibits a considerable linear correlation. Therefore, the inhibition mechanism that 2‐indolinone derivatives were regarded as tubulin inhibitors can be theoretically confirmed. Based on such an inhibition mechanism along with 3D‐QSAR results, some important factors improving the activities of these compounds were discussed in detail. These factors can be summarized as follows: the H atom adopted as substituent R₁, the substituent R₂ with higher electropositivity and smaller bulk, the substituents R₄–R₆ (on the phenyl ring) with higher electropositivity and larger bulk, and so on. These results can offer useful theoretical references for understanding the action mechanism, designing more potent inhibitors, and predicting their activities prior to synthesis. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Insight into the structural requirements of pyrimidine-based phosphodiesterase 10A (PDE10A) inhibitors by multiple validated 3D QSAR approaches

Schizophrenia is a complex disorder of thinking and behaviour (0.3?0.7% of the population is affected). The over-expression of phosphodiesterase 10A (PDE10A) enzyme may be a potential target for schizophrenia and Huntington’s disease. Because 3D QSAR analysis is one of the most frequently used modelling techniques, in the present study, five different 3D QSAR tools, namely CoMFA, CoMSIA, kNN-MFA, Open3DQSAR and topomer CoMFA methods, were used on a dataset of pyrimidine-based PDE10A inhibitors. All developed models were validated internally and externally. The non-commercial Open3DQSAR produced the best statistical results amongst 3D QSAR tools. The structural interpretations obtained from different methods were thoroughly analysed and were justified on the basis of information obtained from the crystal structure. Information from one method was mostly validated by the results of other methods and vice versa. In the current work, the use of multiple tools in the same analysis revealed more complete information about the structural requirements of these compounds. On the basis of the observations of the 3D QSAR studies, 12 new compounds were designed for better PDE10A inhibitory activity. The current investigation may help in further designing new PDE10A inhibitors with promising activity.     

Computational Analysis of CRTh2 receptor antagonist: A Ligand-based CoMFA and CoMSIA approach

CRTh2 receptor is an important mediator of inflammatory effects and has attracted much attention as a therapeutic target for the treatment of conditions such as asthma, COPD, allergic rhinitis and atopic dermatitis. In pursuit of better CRTh2 receptor antagonist agents, 3D-QSAR studies were performed on a series of 2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl) acetic acids. There is no crystal structure information available on this protein; hence in this work, ligand-based comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed by atom by atom matching alignment using systematic search and simulated annealing methods. The 3D-QSAR models were generated with 10 different combinations of test and training set molecules, since the robustness and predictive ability of the model is very important. We have generated 20 models for CoMFA and 100 models for CoMSIA based on two different alignments. Each model was validated with statistical cut off values such as q² > 0.4, r² > 0.5 and r²_pred > 0.5. Based on better q² and r²_pred values, the best predictions were obtained for the CoMFA (model 5 q² = 0.488, r²_pred = 0.732), and CoMSIA (model 45 q² = 0.525, r²_pred = 0.883) from systematic search conformation alignment. The high correlation between the cross-validated/predicted and experimental activities of a test set revealed that the CoMFA and CoMSIA models were robust. Statistical parameters from the generated QSAR models indicated the data is well fitted and have high predictive ability. The generated models suggest that steric, electrostatic, hydrophobic, H-bond donor and acceptor parameters are important for activity. Our study serves as a guide for further experimental investigations on the synthesis of new CRTh2 antagonist.     

New approach to the synthesis of 4-amino-2-pyridone and 1-phenyl-1,6-naphthyridinone derivatives based on substituted 3-and 5-formyl-2-pyridones

The reactions of 3-cyano-3(5)-formyl-2-oxo-4-(phenylamino)-1,2-dihydropyridines with CH acids were studied. The previously unknown fused 2-pyridone derivatives containing the 4-aminopyridine fragment were synthesized by the Knoevenagel reaction. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1416-1420, August, 2006.