Three-dimensional Quantitative Structure-Activity Relationship Analyses of a Series of Butenolide ETA Antagonists

Two kinds of Three-dimensional Quantitative Structure-activity Relationship(3D-QSAR) methods,comparative molecular filed analysis(CoMFA) and comparative molecular similarity indices analysis (CoMSIA) ,were applied to analyze the structure-activity relationship of a series of 63 butenolide ETA selective antagonists with respect to their inhibition against human ETA receptor,The CoMFA and CoMSIA models were developed for the conceivable alignment of the molecules based on a template structure from the crystallized data.The statistical results from the initial orientation of the aligned molecules show that the 3D-QSAR model from CoMFA(q^2=0.543) is obviously superior to that from the conventional CoMSIA(q^2=0.407).In order to refine the model,all-space search (ASS) was applied to minimize the field sampling process.By rotating and translating the molecular aggregate within the grid systematically,all the possible samplings of the molecular fields were tested and subsequently the one with the highest q^2 was picked out .The comparison of the sensitivity of CoMFA and CoMSIA to different space orientation shows that the CoMFA q^2 values are more sensitive to the translations and rotations of the aligned molecules with respect to the lattice than those of CoMSIA.The best CoMFA model from ASS was further refined by the region focused technique.The high quality of the best model is indicated by the high corss-validated correlation and the prediction on the external test set.The CoMFA coefficient contour plots identify several key features that explain the wide range of activities,which may help us to design new effective ETA selective antagonists.     

A 3D‐QSAR Study of Celebrex‐Based Pdk1 Inhibitors Using Comfa Method

A 3D‐QSAR study of celebrex‐based compounds of PDK1 inhibitors using comparative molecular field analysis (CoMFA) was carried out. The structures of the compounds were obtained using quantum chemistry calculation. CoMFA calculations for a number of grouped subsets of compounds gave q² values of correlation in the range from 0 to 0.8. The low q² values should be mainly due to the narrow span of biological activity. Calculations for several subsets of 11–13 compounds gave high q² values, with 0.5–0.8. Factors affecting the results of the calculations are discussed. Calculated results with high q² values suggest that further chemical modifications of the compounds could lead to enhanced activity and could be an aid in the design of celebrex‐based cancer drugs.     

HEPT类逆转录酶抑制剂的三维定量构效关系

利用比较分子力场分析(CoMFA)方法对32个HEPT类HIV-1逆转录酶抑制剂(RTIs)的三维定量构效关系(3D-QSAR)进行了分析,建立了HIV-1逆转录酶抑制剂的3种3D-QSAR模型,发现影响其生物活性的主要因素为立体场因素,这与HIV-1RT的非底物结合部位(NNBS)的疏水性环境相吻合.进一步分析表明,适当长度的1-位侧链对保持化合物的抗病毒活性致关重要;增大5-位取代基的体积可增强生物活性;在1-位苄氧甲基的对位引入大体积基团有利于提高活性.同时考察立体场、静电场与生物活性的关系,表明,CoMFA模型为最佳预测模型,其交叉验证系数R_CV²=0.870,传统相关系数R²=0.986,标准偏差SE=0.146,F=294.546.用此模型预测了检验组3个HEPT类化合物的-lgEC₅₀,R_pred²=0.850,表明模型具有很好的预测能力,可为HEPT类HIV-1逆转录酶抑制剂的结构优化提供理论指导.     

Exploring Amantadine Derivatives as Urease Inhibitors: Molecular Docking and Structure–Activity Relationship (SAR) Studies

This article describes the design and synthesis of a series of novel amantadine-thiourea conjugates (3a–j) as Jack bean urease inhibitors. The synthesized hybrids were assayed for their in vitro urease inhibition. Accordingly, N-(adamantan-1-ylcarbamothioyl)octanamide (3j) possessing a 7-carbon alkyl chain showed excellent activity with IC₅₀ value 0.0085 ± 0.0011 µM indicating that the long alkyl chain plays a vital role in enzyme inhibition. Whilst N-(adamantan-1-ylcarbamothioyl)-2-chlorobenzamide (3g) possessing a 2-chlorophenyl substitution was the next most efficient compound belonging to the aryl series with IC₅₀ value of 0.0087 ± 0.001 µM. The kinetic mechanism analyzed by Lineweaver–Burk plots revealed the non-competitive mode of inhibition for compound 3j. Moreover, in silico molecular docking against target protein (PDBID 4H9M) indicated that most of the synthesized compounds exhibit good binding affinity with protein. The compound 3j forms two hydrogen bonds with amino acid residue VAL391 having a binding distance of 1.858 Å and 2.240 Å. The interaction of 3j with amino acid residue located outside the catalytic site showed its non-competitive mode of inhibition. Based upon these results, it is anticipated that compound 3j may serve as a lead structure for the design of more potent urease inhibitors.     

3D‐QSAR studies and molecular design on a novel series of pyrimidine benzimidazoles as Lck inhibitors

The development of selective lymphocyte‐specific kinase (Lck) inhibitors has attracted much attention for the research of the treatment of T‐cell mediated autoimmune and inflammatory diseases. In the present work, three‐dimensional quantitative structure–activity relationship (3D‐QSAR) analyses are performed on a novel series of 4‐amino‐6‐benzimidazole‐pyrimidines acting as Lck inhibitors. The established 3D‐QSAR models show significant statistical quality and satisfactory predictive ability, with high q² and R² values: the comparative molecular field analysis (CoMFA) model (q² = 0.802, R² = 0.991), and the comparative molecular similarity indexes analysis (CoMSIA) model (q² = 0.731, R² = 0.982). The systemic external validation indicates that both CoMFA and CoMSIA models are quite robust and possess high predictive abilities with values of 0.881 and 0.877, values of 0.897 and 0.847, values of 0.897 and 0.850, and values of 0.897 and 0.854, respectively. Several key structural features accounting for the inhibitory activities of these compounds are discussed. Based on established models and design considerations, six new compounds with significantly improved activities are theoretically designed, which still await experimental confirmation and evaluation. These theoretical results may provide a useful reference for understanding the action mechanism and designing novel potential Lck inhibitors. © 2014 Wiley Periodicals, Inc.     

Synthesis,Bioactivities and Structure Activity Relationship of N‐4‐Methyl‐1,2,3‐thiadiazole‐5‐carbonyl‐N′‐phenyl Ureas

Twenty nine novel N‐4‐methyl‐1,2,3‐thiadiazole‐5‐carbonyl‐N′‐phenyl ureas were designed and synthesized, and their structures were confirmed by proton nuclear magnetic resonance (¹H NMR), infra red spectroscopy (IR) and high‐resolution mass spectroscopy (HRMS). Compounds V‐9 , V‐11 , V‐12 , V‐15 , V‐19 , V‐21 , V‐22 and V‐24 exhibit excellent activity against Culex pipiens pallens. Compounds V‐12 and V‐22 present good insecticidal activity against Plutella xylostella L. Their median lethal concentrations (LC₅₀) are 164.15 and 89.69 mg·L^?1, respectively. Compound V‐11 also has potential wide spectrum of fungicide activity. Its median effective concentrations (EC₅₀) detected from 3.82 µg·mL^?1 against Physalospora piricola to 31.60 µg·mL^?1 against Cercospora arachidicola. Compounds V‐15 and V‐24 show outstanding induction activities as same as positive controls TDL and ningnanmycin, furthermore V‐24 has the highest induction activity of 41.85%±4.43%. To elucidate the structure activity relationship in these compounds, a 3D‐QSAR model has been built. The established model showed a reliable predicting ability with q² values of 0.643 and r² values of 0.982.     

Synthesis,Nematicidal Activity,and 3D‐QSAR of Novel 1,3,4‐Oxadiazole/ Thiadiazole Thioether Derivatives

Forty one novel 1,3,4‐oxadiazole/thiadiazole thioether derivatives containing phenoxy moiety were designed and synthesized. Bioassay demonstrated that some of them showed remarkable activities against Tylenchulus semipenetrans in vitro and in vivo. Compounds 20 , 21 , 35 and 39 showed excellent lethal activities after treatment for 48 h in vitro, with LC₅₀ values of 13.4 ± 1.8, 11.7 ± 2.5, 13.7 ± 2.4 and 13.3 ± 1.1 mg·L^–1, respectively, which were obviously superior to fosthiazate (49.1 ± 2.8 mg·L^–1) and avermectin (26.6 ± 2.3 mg·L^–1). Compound 21 can effectively control the citrus nematode disease caused by T. semipenetrans at 200 mg·L^–1 in vivo with (68 ± 3)% inhibitory effect, which was even better than that of avermectin ((63 ± 2)%). The CoMFA and CoMSIA models of three‐dimensional quantitative structure‐activity relationships (3D‐QSARs) were established. The compound 33 was designed based on the 3D‐QSAR models with more vigorous nematicidal activities in vitro (LC₅₀ = 9.8 ± 1.4 mg·L^–1) and in vivo ((70 ± 5)%). These results demonstrated that compound 33 can be considered as a potential nematicide.     

QSAR,Molecular Docking,MD Simulation and MMGBSA Calculations Approaches to Recognize Concealed Pharmacophoric Features Requisite for the Optimization of ALK Tyrosine Kinase Inhibitors as Anticancer Leads

ALK tyrosine kinase ALK TK is an important target in the development of anticancer drugs. In the present work, we have performed a QSAR analysis on a dataset of 224 molecules in order to quickly predict anticancer activity on query compounds. Double cross validation assigns an upward plunge to the genetic algorithm–multi linear regression (GA-MLR) based on robust univariate and multivariate QSAR models with high statistical performance reflected in various parameters like, fitting parameters; R² = 0.69–0.87, F = 403.46–292.11, etc., internal validation parameters; Q²_LOO = 0.69–0.86, Q²_LMO = 0.69–0.86, CCC_cv = 0.82–0.93, etc., or external validation parameters Q²_F1 = 0.64–0.82, Q²_F2 = 0.63–0.82, Q²_F3 = 0.65–0.81, R²_ext = 0.65–0.83 including RMSE_tr < RMSE_cv. The present QSAR evaluation successfully identified certain distinct structural features responsible for ALK TK inhibitory potency, such as planar Nitrogen within four bonds from the Nitrogen atom, Fluorine atom within five bonds beside the non-ring Oxygen atom, lipophilic atoms within two bonds from the ring Carbon atoms. Molecular docking, MD simulation, and MMGBSA computation results are in consensus with and complementary to the QSAR evaluations. As a result, the current study assists medicinal chemists in prioritizing compounds for experimental detection of anticancer activity, as well as their optimization towards more potent ALK tyrosine kinase inhibitor.     

Design of Novel IRAK4 Inhibitors Using Molecular Docking,Dynamics Simulation and 3D-QSAR Studies

Treatment of several autoimmune diseases and types of cancer has been an intense area of research over the past two decades. Many signaling pathways that regulate innate and/or adaptive immunity, as well as those that induce overexpression or mutation of protein kinases, have been targeted for drug discovery. One of the serine/threonine kinases, Interleukin-1 Receptor Associated Kinase 4 (IRAK4) regulates signaling through various Toll-like receptors (TLRs) and interleukin-1 receptor (IL1R). It controls diverse cellular processes including inflammation, apoptosis, and cellular differentiation. MyD88 gain-of-function mutations or overexpression of IRAK4 has been implicated in various types of malignancies such as Waldenström macroglobulinemia, B cell lymphoma, colorectal cancer, pancreatic ductal adenocarcinoma, breast cancer, etc. Moreover, over activation of IRAK4 is also associated with several autoimmune diseases. The significant role of IRAK4 makes it an interesting target for the discovery and development of potent small molecule inhibitors. A few potent IRAK4 inhibitors such as PF-06650833, RA9 and BAY1834845 have recently entered phase I/II clinical trial studies. Nevertheless, there is still a need of selective inhibitors for the treatment of cancer and various autoimmune diseases. A great need for the same intrigued us to perform molecular modeling studies on 4,6-diaminonicotinamide derivatives as IRAK4 inhibitors. We performed molecular docking and dynamics simulation of 50 ns for one of the most active compounds of the dataset. We also carried out MM-PBSA binding free energy calculation to identify the active site residues, interactions of which are contributing to the total binding energy. The final 50 ns conformation of the most active compound was selected to perform dataset alignment in a 3D-QSAR study. Generated RF-CoMFA (q² = 0.751, ONC = 4, r² = 0.911) model revealed reasonable statistical results. Overall results of molecular dynamics simulation, MM-PBSA binding free energy calculation and RF-CoMFA model revealed important active site residues of IRAK4 and necessary structural properties of ligand to design more potent IRAK4 inhibitors. We designed few IRAK4 inhibitors based on these results, which possessed higher activity (predicted pIC₅₀) than the most active compounds of the dataset selected for this study. Moreover, ADMET properties of these inhibitors revealed promising results and need to be validated using experimental studies.     

Design and Synthesis of 3‐Aryl‐5‐Alicylic‐[1,2,4]‐oxadiazoles as Novel Platelet Aggregation Inhibitors

A series of 4‐[2‐(alicyclic‐[1,2,4]oxadiazol‐3‐yl)phenoxy]‐butyric acids were synthesized from N‐hydroxy‐2‐isopropoxy benzamidine in 4 steps with good yields. These [1,2,4]oxadiazoles are novel platelet aggregation inhibitors preventing human platelet aggregation induced by thromboxane derivative U44,619 and adenosine diphosphate. A structure‐activity‐relationship study revealed that the potency for these 5‐oxadiazoles increases with the increase in the ring size of the alicylic rings. Derivative 8f may be useful as a template for the design of more potent anti‐platelet agents.     

A Simple Synthesis of Polyfunctionalized 4‐Aminopyrazolidin‐3‐ones as ‘Aza‐deoxa’ Analogs of D‐Cycloserine

A simple five‐step synthesis of fully substituted (4RS,5RS)‐4‐aminopyrazolidin‐3‐ones as analogs of D ‐cycloserine was developed. It comprises a two‐step preparation of 5‐substituted (4RS,5RS)‐4‐(benzyloxycarbonylamino)pyrazolidin‐3‐ones, reductive alkylation at N(1), alkylation of the amidic N(2) with alkyl halides, and simultaneous hydrogenolytic deprotection/reductive alkylation of the primary NH₂ group. The synthesis enables an easy stepwise functionalization of the pyrazolidin‐3‐one core with only two types of common reagents, aldehydes (or ketones) and alkyl halides. The structures of products were elucidated by NMR spectroscopy and X‐ray diffraction.     

Synthesis of a Novel Series of 2,3‐Disubstituted Quinazolin‐4(3H)‐ones as a Product of a Nucleophilic Attack at C(2) of the Corresponding 4H‐3,1‐Benzoxazin‐4‐one

A new series of 2,3‐disubstituted quinazolin‐4(3H)‐one derivatives was synthesized by nucleophilic attack at C(2) of the corresponding key starting material 2‐propyl‐4H‐3,1‐benzoxazin‐4‐one (Scheme 2). The reaction proceeded via amidinium salt formation (Scheme 3) rather than via an N‐acylanthranilimide. The structure of the prepared compounds were elucidated by physical and spectral data like FT‐IR, ¹H‐NMR, and mass spectroscopy.     

Molecular Design of D‐π‐A Type II Organic Sensitizers for Dye Sensitized Solar Cells

Four new type II organic dyes with D‐π‐A structure (donor‐π‐conjugated‐acceptor) and two typical type II sensitizers based on catechol as reference dyes are synthesized and applied in dye sensitized solar cells (DSCs). The four dyes can be adsorbed on TiO₂ through hydroxyl group directly. Electron injection can occur not only through the anchoring group (hydroxyl group) but also through the electron‐withdrawing group (? CN) located close to the semiconductor surface. Experimental results show that the type II sensitizers with a D‐π‐A system obviously outperform the typical type II sensitizers providing much higher conversion efficiency due to the strong electronic push‐pull effect. Among these dyes, LS223 gives the best solar energy conversion efficiency of 3.6%, with J_sc=7.3 mA·cm^?2, V_oc=0.69 V, FF=0.71, the maximum IPCE value reaches 74.9%.     

One‐Pot Regioselective Synthesis of Novel Oximino Ester‐Containing 1‐Aryl‐4‐chloro‐3‐oxypyrazoles as Potential Fungicides

A novel, functional‐group‐tolerant, and highly regioselective one‐pot synthesis of six 4‐chloro‐1‐aryl‐3‐oxypyrazoles, 8a – 8f , containing an oximino ester moiety has been developed. Their structures were characterized by ¹H‐ and ¹³C‐NMR, IR, MS, and elemental analyses. The regioselectivity of the reaction was also determined by single‐crystal X‐ray diffraction analysis of product 8d . The reaction pathway, proposed with the aid of DFT calculations, likely proceeds via a DMF‐catalyzed mechanism, which involves an electrophilic attack by SOCl₂ and two nucleophilic substitutions by benzyl bromide (BnBr) and Cl^?, respectively, as the key steps. A preliminary in vitro bioassay indicated that most compounds exhibited good fungicidal activities against Sclerotinia sclerotiorum and Gibberella zeae. Especially, 8d and 8e displayed higher or similar fungicidal activities compared with pyraclostrobin at the concentration of 10 μg/ml.