Neuronal nicotinic receptor agonists: a multi-approach development of the pharmacophore

Based on the results obtained with different automated computational approaches as applied to the study of eleven high-affinity agonists of the neuronal nicotine acetylcholine receptor (nAChR), belonging to different chemical classes, new relevant features were detected which complement the existing pharmacophores. Convergent results from DISCO (Distance Comparison), QXP (Quick Explore), Catalyst/HipHop, and MIPSIM (Molecular Interaction Potential Similarity) allowed us to identify and locate, in a well defined spatial arrangement, three geometrically independent key structural features: (i) a positively charged nitrogen atom for ionic or hydrogen bond interactions, (ii) a lone pair of the pyridine nitrogen or a specific lone pair of a carbonyl oxygen, as a hydrogen bond acceptor, and (iii) a centre of a hydrophobic area generally occupied by aliphatic cycles. The pharmacophore presented herein, along with predictive 2D and 3D QSAR models recently developed in our group, could represent valuable computational tools for the design of new nAChR agonists having therapeutical potential.     

Selective ATP competitive leads of CDK4: Discovery by 3D-QSAR pharmacophore mapping and molecular docking approach

The discovery of ATP competitive CDK4 inhibitors is an on-going challenging task in cancer therapy. Here, an attempt has been made to develop new leads targeting ATP binding site of CDK4 by applying 3D-QSAR pharmacophore mapping and molecular docking methods The outcome of 6 leads offers a significant contribution for selective CDK4 inhibition, since they show potential binding interactions with Val⁹⁶, Arg¹⁰¹, and Glu¹⁴⁴ residues of CDK4, that are unique and from other kinases. It is worth noting that there is a striking similarity in binding interactions of the leads and known CDK4 inhibitors, namely Abemaciclib, Palbociclib and Ribociclib. Further key features, including high dock score value, good predicted activity, scaffold diversity, and the acceptable ADME profile of leads, provide a great opportunity for the development of highly potent and selective ATP competitive inhibitors of CDK4.     

Cytisine: a natural product lead for the development of drugs acting at nicotinic acetylcholine receptors

Covering: up to the end of 2011. This review covers classical and modern structural modifications of the alkaloid, the more recent (since 2007) syntheses of cytisine and analogues, and the pharmacology of these compounds, with emphasis on their interactions with nicotinic receptors. 89 references are cited.     

Molecular modelling studies on adamantane-based Ebola virus GP-1 inhibitors using docking,pharmacophore and 3D-QSAR

The pathogenic Ebola virus (EBOV) causes a potential health risk and global spread. To date, few drugs are available for the treatment of Ebola virus disease (EVD) that allow researchers to use computational methods for designing potential drugs. The developed PHASE-based common six-point pharmacophore hypothesis (AADHPR_1) showed the necessity of two hydrogen bond acceptor features, one hydrogen bond donor feature, one hydrophobic group feature, one positively ionizable and one aromatic ring feature for further designing. We developed best 3D-QSAR models with high regression coefficients for the training (r²>0.82) and test (Q²>0.5) sets for both atoms-based and field-based 3D-QSAR models. The molecule 1A-4 (docking score = –4.711 kcal/mol) was obtained as best docked (SP mode) on Ebola virus envelope glycoprotein (PDB ID-3CSY) as compared with the standards oseltamivir (docking score = –4.39 kcal/mol) and zanamivir (docking score = –3.392 kcal/mol). The obtained ZINC hit ZINC58935541 showed a good docking score of –4.892 kcal/mol. The ZINC58935541 molecule also showed a strong binding affinity towards the receptor cavity of Ebola virus envelope glycoprotein when simulated for 1.2 ns. The good QikProp parameters reflect the fact that this molecule, upon optimization into a lead, might become a good candidate for the treatment of EVD.     

3D-QSAR Study on a Series of Indolo[1,2-b]quinazoline Derivatives with Anticancer Activity and their Molecular Design

Indolo[1,2-b]quinazoline derivatives have recently been reported as a type of compound with potential anticancer activity. On the basis of our the published two-dimensional quantitative structure-activity relationship (2D-QSAR) of these compounds, a further study on the three-dimensional quantitative structure-activity relationship (3D-QSAR) was carried out using the method of comparative molecular field analysis (CoMFA). A reasonable, receivable, and an effective 3D-QSAR model has been established, in which the correlation coefficient (r²) and cross-validation coefficient (q²) values are 0.986 and 0.695, respectively, the statistical squared deviation ratio (F) is 114.6, and the standard deviation (SD) is 0.084. The results suggest that the electrostatic effect of substituent R₁ and steric effect of substituent R₂ play a very important role in the improvement of the anticancer activity of these compounds. In this article, some significant conclusions, which are in good agreement with the conclusions obtained using 2D-QSAR, were drawn as follows. (1) The electrostatic effect in the substituent R₁ part plays a major role, and it is very important to make the first atom of R₁ carrying more positive charges in order to improve the anticancer activity of the compounds. (2) The steric effect plays a major role in the substituent R₂ part, and the volume of R₂ should be moderate. Based on the above conclusions, three new molecules of Indolo[1,2-b]quinazoline derivatives with higher anticancer activity have been theoretically designed and are waiting for support from experiment. The QSAR results can offer a theoretical reference for the pharmaceutical synthesis.     

Identification of potential Gly/NMDA receptor antagonists by cheminformatics approach: a combination of pharmacophore modelling,virtual screening and molecular docking studies

The Gly/NMDA receptor has become known as potential target for the management of neurodegenerative diseases. Discovery of Gly/NMDA antagonists has thus attracted much attention in recent years. In the present research, a cheminformatics approach has been used to determine structural requirements for Gly/NMDA antagonism and to identify potential antagonists. Here, 37 quinoxaline derivatives were selected to develop a significant pharmacophore model with good certainty. The selected model was validated by leave-one-out cross-validation, an external test set, decoy set and Y-randomization test. Applicability domain was verified by the standardization approach. The validated 3D-QSAR model was used to screen virtual hits from the ZINC database by pharmacophore mapping. Molecular docking was used for assessment of receptor–ligand binding modes and binding affinities. The GlideScore and molecular interactions with critical amino acids were considered as crucial features to identify final hits. Furthermore, hits were analysed for in silico pharmacokinetic parameters and Lipinski’s rule of five, demonstrating their potential as drug-like candidates. The PubChem and SciFinder search tools were used to authenticate the novelty of leads retrieved. Finally, five different leads have been suggested as putative novel candidates for the exploration of potent Gly/NMDA receptor antagonists.     

抗癌性吲哚喹唑啉衍生物3D-QSAR研究及其分子设计

吲哚喹唑啉衍生物是近年来发现的一类具有良好抗癌活性的化合物. 作者在最近报道的二维定量构效关系(2D-QSAR)的基础上, 采用比较分子力场方法(CoMFA)进一步对该系列化合物进行三维定量构效关系(3D-QSAR)研究, 建立了3D-QSAR的CoMFA模型, 其非交叉验证相关系数r2=0.986, 标准偏差SD=0.084, 统计方差比F=114.6, 交叉验证相关系数q2=0.695, 表明该模型合理、可信, 并具有良好的预测能力. 研究结果表明: (1) 取代基R1的部位上静电效应起主要作用, 并且确保取代基R1的第一个原子具有较大的净正电荷, 对提高化合物的抗癌活性十分重要. 这与2D-QSAR研究结果相一致. (2) 取代基R2的部位上立体效应起主要作用, R2的体积大小要适中. 应用这些规律进行了分子设计, 在理论上获得了一些具有较高抗癌活性的新的吲哚喹唑啉衍生物, 并期待实验证实. 该QSAR的研究结果可为实验工作者合成新药提供理论参考.     

A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method

CoMFA analysis, a widely used 3D-QSAR method, has limitations to handle a set of SAR data containing diverse conformational flexibility since it does not explicitly include the conformational entropic effects into the analysis. Here, we present an attempt to incorporate the conformational entropy effects of a molecule into a 3D-QSAR analysis. Our attempt is based on the assumption that the conformational entropic loss of a ligand upon making a ligand-receptor complex is small if the ligand in an unbound state has a conformational propensity to adopt an active conformation in a complex state. For a QSAR analysis, this assumption was interpreted as follows: a potent ligand should have a higher conformational propensity to adopt an `active-conformation'-like structure in an unbound state than an inactive one. The conformational propensity value was defined as the populational ratio, N<sub>active</sub>/N<sub>stable</sub>, of the number of energetically stable conformers, N<sub>stable</sub>, to the number of `active-conformation'-like structures, N_active. The latter number was calculated by counting the number of conformers that satisfied the structural parameters deduced from the active conformation. A set of SAR data of imidazoleglycerol phosphate dehydratase inhibitors containing 20 molecules with different conformational flexibility was used as a training set for developing a 3D structure-activity relationship by a CoMFA analysis with the conformational propensity value. This resulted in a cross-validated squared correlation coefficient of the CoMFA model with the conformational propensity value (R ² _cross = 0.640) higher than that of the standard CoMFA model (R ² _cross = 0.431). Then we evaluated the quality of the CoMFA models by predicting the inhibitory activity for a new molecule.     

Molecular docking,dynamics simulations and 3D-QSAR modeling of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT1AR agonists

Serotonin receptor, 5-HT_1AR, agonists and partial agonists have established drug candidates for psychiatric and neurologic disorders. Recently, we reported the synthesis and evaluation of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT_1AR ligands. Herein, we generated a homology model of the receptor and docked the ligands against it, predicted the stability of the receptor model and complexes by molecular dynamics and generated a 3D-QSAR model for the arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine. The model suggests the hydrophobic part that arises from the aromatic region and the electron withdrawing parts play a vital role in the agonist activity of the lead molecules.     

Fe3O4@MCM-48–SO3H:合成苯并[f]色烯并[2,3-d]嘧啶酮的高效、可磁性分离纳米催化剂（英文）

Sulfonic acid groups were grafted onto three different types of synthesized magnetic nanoparticles, namely Fe3O4, Fe3O4@SiO2, and Fe3O4@MCM‐48. The sulfonic acid‐functionalized nanoparticles were evaluated as catalysts for the synthesis of 5‐aryl‐1H‐benzo[f]chromeno[2,3‐d]pyrimidine‐2,4(3H,5H)‐dione derivatives in terms of activity and recyclability. Their catalytic activities were compared with that of the homogeneous acid catalyst 1‐methylimidazolium hydrogen sulfate ([HMIm][HSO4]). The activity of Fe3O4@MCM‐48–SO3H was comparable to those of the other heter‐ogeneous and homogeneous catalysts.     

Fe3O4@MCM-48-SO3H:An efficient magnetically separable nanocatalyst for the synthesis of benzo[f]chromeno[2,3-d]pyrimidinones

Sulfonic acid groups were grafted onto three different types of synthesized magnetic nanoparticles, namely Fe3O4, Fe3O4@SiO2, and Fe3O4@MCM‐48. The sulfonic acid‐functionalized nanoparticles were evalu...     

An improved and scalable process for 3,8-diazabicyclo[3.2.1]-octane analogues

An improved and scalable process for substituted 3,8-diazabicyclo[3.2.1]octane was developed.N-Benzyl-2,5-dicarbethoxy-pyrrolidine 2 was reduced to N-benzyl-2.5-dihydroxymethylpyrrolidine 9 and subsequently debenzylated to afford N-Boc-2,5- dihydroxymethylpyrrolidine 10.After mesylation of the diol 10 and cyclization with benzylamine,a diversity of scaffold,3,8- diazabicyclo[3.2.1]octane analogue 12 was obtained in a total yield of 42%in five steps.     

An expedient approach for the regio- and stereoselective synthesis of novel spiroindolizidines via [3+2] cycloaddition

A new series of spiroindolizidines was synthesized by one-pot, three-component condensation of azomethine ylides, generated from 1,2,3,4-tetrahydroisoquinoline with ninhydrin or isatin derivatives by a 1,5-prototropic shift route, with various derivatives of trans-β-nitrostyrene in a regio- and stereoselective manner. X-ray crystal structure analysis and NMR spectroscopic data confirmed the structure outcome of the cycloaddition reaction.     

Evidence from ESR studies for [Co(eta-C2H4)3] produced at 77 K in a rotating cryostat

Co atoms were reacted with ethene at 77 K and the paramagnetic products studied by electron spin resonance (ESR) at X- and K-bands. The ESR spectra of the major product at both frequencies showed eight cobalt multiplets (ICo=7/2) indicating a mono-cobalt complex. The spectra have orthorhombic g and cobalt hyperfine tensors and were simulated by the parameters; g1=2.284, g2=2.0027, g3=2.1527; A1<-25 MHz, A2=-109 MHz, A3=-198 MHz. Proton and 13C (1% natural abundance) hyperfine couplings were lower than the line widths (<2 MHz) indicating less than 0.5 spin transfer to the ethene ligands. We assigned the spectrum to a Jahn-Teller-distorted planar trigonal mono-cobalt tris-ethene [Co(eta-C2H4)3] complex in C2v symmetry. The SOMO is either a 3dx2-y2 (2a1) orbital in a T-geometry or a 3dxy (b1) orbital in a Y-geometry but there is only a spin density, a2, of 0.30 in these d orbitals. The spin deficiency of 0.70 is attributed to two factors; spin transfer from the Co to ethene pi/pi* orbitals and a 4p orbital contribution, b2, to the SOMO. Calculations of a2 and b2 have been made at three levels of spin transfer, theta. At theta=0.00a2 is 0.23 and b2 is 0.78, at theta=0.25a2 is 0.25 and b2 is 0.52 and at theta=0.50a2 is 0.28 and b2 is 0.23. The other possible assignment to a mono-cobalt bis-ethene complex [Co(eta-C2H4)2] cannot be discounted from the ESR data alone but is considered unlikely on other grounds. The complex is stable up to approximately 220 K indicating a barrier to decomposition of approximately 50 kJ Mol-1     

苯环5位取代磺酰脲类化合物的水解动力学及三维定量构效关系初步研究

研究了除草活性较好的9个新型苯环5位取代的磺酰脲类化合物(A~I)分别在酸性、中性及碱性水溶液中的水解情况.采用HPLC-MS对水解产物进行分离鉴定,推测了水解产物的结构及水解路径.采用比较分子力场(Co MFA)方法,对化合物的结构与水解半衰期之间的关系进行了三维定量构效关系(3D-QSAR)研究.结果表明,苯环5位取代的苯磺酰脲类化合物的水解遵循一级动力学反应,容易发生酸性条件下的水解,水解反应第一步主要为酸催化下磺酰脲桥的断裂,形成5位取代的苯磺酰胺和氨基杂环.苯环5位取代的苯磺酰胺进一步发生5位酰胺基的水解,最后得到化合物c(6-氨基糖精)和d(糖精).苯环5位经修饰改造后,在相同条件下,其水解速度明显高于改造前的母体化合物单嘧磺酯和甲磺隆.苯环5位为酰胺基取代的化合物的水解速度随酰胺基上烷基碳原子数的增加及烷基体积的增大而降低.经计算所得的Co MFA模型能够对该系列化合物的水解半衰期进行较好的预测.     

Imidazo[1,2-a]pyrazine inhibitors of phosphoinositide 3-kinase alpha (PI3Kα): 3D-QSAR analysis utilizing the Hybrid Monte Carlo algorithm to refine receptor-ligand complexes for molecular alignment

Phosphoinositide 3-kinase alpha (PI3Kα) is a lipid kinase involved in several cellular functions such as cell growth, proliferation, differentiation and survival, and its anomalous regulation leads to cancerous conditions. PI3Kα inhibition completely blocks the cancer signalling pathway, hence it can be explored as an important therapeutic target for cancer treatment. In the present study, docking analysis of 49 selective imidazo[1,2-a]pyrazine inhibitors of PI3Kα was carried out using the QM-Polarized ligand docking (QPLD) program of the Schrödinger software, followed by the refinement of receptor–ligand conformations using the Hybrid Monte Carlo algorithm in the Liaison program, and alignment of refined conformations of inhibitors was utilized for the development of an atom-based 3D-QSAR model in the PHASE program. Among the five generated models, the best model was selected corresponding to PLS factor 2, displaying the highest value of Q²_test (0.650). The selected model also displayed high values of r²_train (0.917), F-value (166.5) and Pearson-r (0.877) and a low value of SD (0.265). The contour plots generated for the selected 3D-QSAR model were correlated with the results of docking simulations. Finally, this combined information generated from 3D-QSAR and docking analysis was used to design new congeners.     

H14[NaP5W30O110] as a Heterogeneous Recyclable Catalyst for the Synthesis of 6,8-Dimethyl-3-aryl-[1,2,4]triazolo[3,4-b][1,3,4]thiazepine Derivatives

6,8-Dimethyl-3-aryl-[1,2,4]triazolo[3,4-b][1,3,4]thiazepine derivatives were synthesized by cyclodehydration of 3-aryl-4-amino-5-mercapto-1,2,4-triazole with 2,4-pentanedione in the presence of a catalytic amount of Preyssler catalyst under very mild conditions.     

Fused heterocycles. 8 . An efficient procedure for the stereoselective synthesis of trans-2,3,3a,4-tetrahydro-3-aryl-2-phenyl[1]benzopyrano[4,3-c]pyrazoles and their [1]benzothiopyrano analogues

Stereoselective synthesis of trans-2,3,3a,4-tetrahydro-3-aryl-2-phenyl[1]benzopyrano[4,3-c]pyrazoles 13–18 and their [1]benzothiopyrano analogues 19–24 has been performed by the reaction of 3-arylidenechromanones 1–6 and 3-arylidene-1-thiochromanones 7–12 with phenylhydrazine in hot pyridine. The structure and stereochemistry of the compounds prepared have been elucidated by ir, ^lH and ¹³C nmr measurements.