3D-QSAR and docking studies on 2-arylbenzoxazole and linker-Y transthyretin amyloidogenesis inhibitors

Transthyretin (TTR), a plasma protein with a tetramer structure, could form amyloid fibril associated with several human diseases through the dissociation of tetramer and the misfolding of monomer. These amyloidogenesis can be inhibited by small molecules which bind to the central channel of TTR. A number of small molecules like 2-arylbenzoxazoles (ABZ) analogues are proposed as promising therapeutic strategy to treat amyloidosis. In this work, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) three-dimensional quantitative structure-activity relationship (3D-QSAR) and docking studies were performed on series of 2-arylbenzoxazoles (ABZ) and linker-Y analogues to investigate the inhibitory activities of TTR amyloidogenesis at atomic level. Significant correlation coefficients for ABZ series (CoMFA, r ² = 0.877, q ² = 0.431; CoMSIA, r ² = 0.836, q ² = 0.447) and those for linker-Y series (CoMFA, r ² = 0.828, q ² = 0.522; CoMSIA, r ² = 0.800, q ² = 0.493) were obtained, and the generated models were validated using test sets. In addition, docking studies on 6 compounds binding to TTR were performed to analyze the forward or reverse binding mode and interactions between molecules and TTR. These results from 3D-QSAR and docking studies have great significance for designing novel TTR amyloidogenesis inhibitors in the future.     

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.     

CoMFA and CoMSIA studies on a new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line

Abstract  A new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line is examined to determine the relationship between the structural properties and the biological activity of these compounds—the 3-D quantitative structure–activity relationship (3D-QSAR)—using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best CoMFA and CoMSIA models were obtained using the atom-based alignment of 33 compounds, 22 training compounds and 11 tested compounds, and these give desirable statistics; those for the CoMFA standard model were: r _cv² = 0.691, r ² = 0.998, S _press = 0.178, s = 0.014 and F = 1080.765, while CoMSIA combined steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields: r _cv² = 0.600, r ² = 0.988, S _press = 0.206, s = 0.034 and F = 284.433. The 3D-QSAR models calculated satisfactory test set activities. The 3D-QSAR contour plots correlated strongly with the experimental data for the binding topology. For this reason, these results would be beneficial for predicting affinities with the compounds of interest, and they are advantageous for guiding the design and synthesis of new and more effective anticancer agents. Graphical abstract   A new and more effective anticancer agent of xanthone derivatives against the oral human epidermoid carcinoma (KB) cell line, as investigated by CoMFA and CoMSIA analysis     

Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: a molecular modeling study

The p38 protein kinase is a serine–threonine mitogen activated protein kinase, which plays an important role in inflammation and arthritis. A combined study of 3D-QSAR and molecular docking has been undertaken to explore the structural insights of pyrazolyl urea p38 kinase inhibitors. The 3D-QSAR studies involved comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA). The best CoMFA model was derived from the atom fit alignment with a cross-validated r ² (q ²) value of 0.516 and conventional r ² of 0.950, while the best CoMSIA model yielded a q ² of 0.455 and r ² of 0.979 (39 molecules in training set, 9 molecules in test set). The CoMFA and CoMSIA contour maps generated from these models provided inklings about the influence of interactive molecular fields in the space on the activity. GOLD, Sybyl (FlexX) and AutoDock docking protocols were exercised to explore the protein–inhibitor interactions. The integration of 3D-QSAR and molecular docking has proffered essential structural features of pyrazolyl urea inhibitors and also strategies to design new potent analogues with enhanced activity.     

Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: <Emphasis Type="Italic">Plasmodium Falciparum</Emphasis> cysteine proteases inhibitors

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were conducted on a series (39 molecules) of peptidyl vinyl sulfone derivatives as potential Plasmodium Falciparum cysteine proteases inhibitors. Two different methods of alignment were employed: (i) a receptor-docked alignment derived from the structure-based docking algorithm GOLD and (ii) a ligand-based alignment using the structure of one of the ligands derived from a crystal structure from the PDB databank. The best predictions were obtained for the receptor-docked alignment with a CoMFA standard model (q ² = 0.696 and r ² = 0.980) and with CoMSIA combined electrostatic, and hydrophobic fields (q ² = 0.711 and r ² = 0.992). Both models were validated by a test set of nine compounds and gave satisfactory predictive r ² _pred values of 0.76 and 0.74, respectively. CoMFA and CoMSIA contour maps were used to identify critical regions where any change in the steric, electrostatic, and hydrophobic fields may affect the inhibitory activity, and to highlight the key structural features required for biological activity. Moreover, the results obtained from 3D-QSAR analyses were superimposed on the Plasmodium Falciparum cysteine proteases active site and the main interactions were studied. The present work provides extremely useful guidelines for future structural modifications of this class of compounds towards the development of superior antimalarials.     

CoMFA,CoMSIA, Topomer CoMFA,HQSAR, molecular docking and molecular dynamics simulations study of triazine morpholino derivatives as mTOR inhibitors for the treatment of breast cancer

mTOR has become a promising target for many types of cancer like breast, lung and renal cell carcinoma. CoMFA, CoMSIA, Topomer CoMFA and HQSAR were performed on the series of 39 triazine morpholino derivatives. CoMFA analysis showed q² value of 0.735, r²_cv value of 0.722 and r²_pred value of 0.769. CoMSIA analysis (SEHD) showed q² value of 0.761, r²_cv value of 0.775 and r²_pred value of 0.651. Topomer CoMFA analysis showed q² value of 0.693, r² (conventional correlation coefficient) value of 0.940 and r²_pred value of 0.720. HQSAR analysis showed q²,r²and r²_pred values of 0.694, 0.920 and 0.750, respectively. HQSAR analysis with the combination of atomic number (A), bond type (B) and atomic connections showed q² and r² values of 0.655 and 0.891, respectively. Contour maps from all studies provided significant insights. Molecular docking studies with molecular dynamics simulations were carried out on the highly potent compound 36. Furthermore, four acridine derivatives were designed and docking results of these designed compounds showed the same interactions as that of the standard PI-103 which proved the efficiency of 3D-QSAR and MD/MS study. In future, this study might be useful prior to synthesis for the designing of novel mTOR inhibitors.     

Comparative QSAR studies using HQSAR,CoMFA, and CoMSIA methods on cyclic sulfone hydroxyethylamines as BACE1 inhibitors

The inhibition of β-secretase (BACE1) is currently the main pharmacological strategy available for Alzheimer’s disease (AD). 2D QSAR and 3D QSAR analysis on some cyclic sulfone hydroxyethylamines inhibitors against β-secretase (IC₅₀: 0.002–2.75 μM) were carried out using hologram QSAR (HQSAR), comparative molecular field analysis (CoMFA), and comparative molecular similarity indices analysis (CoMSIA) methods. The best model based on the training set was generated with a HQSAR q² value of 0.693 and r² value of 0.981; a CoMFA q² value of 0.534 and r² value of 0.913; and a CoMSIA q² value of 0.512 and r² value of 0.973. In order to gain further understand of the vital interactions between cyclic sulfone hydroxyethylamines and the protease, the analysis was performed by combining the CoMFA and CoMSIA field distributions with the active sites of the BACE1. The final QSAR models could be helpful in the design and development of novel active BACE1 inhibitors.     

CoMFA and CoMSIA studies on a new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line

Abstract  

A new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line is examined to determine the relationship between the structural properties and the biological activity of these compounds—the 3-D quantitative structure–activity relationship (3D-QSAR)—using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best CoMFA and CoMSIA models were obtained using the atom-based alignment of 33 compounds, 22 training compounds and 11 tested compounds, and these give desirable statistics; those for the CoMFA standard model were: r _cv² = 0.691, r ² = 0.998, S _press = 0.178, s = 0.014 and F = 1080.765, while CoMSIA combined steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields: r _cv² = 0.600, r ² = 0.988, S _press = 0.206, s = 0.034 and F = 284.433. The 3D-QSAR models calculated satisfactory test set activities. The 3D-QSAR contour plots correlated strongly with the experimental data for the binding topology. For this reason, these results would be beneficial for predicting affinities with the compounds of interest, and they are advantageous for guiding the design and synthesis of new and more effective anticancer agents.     

3D-QSAR and molecular docking study of LRRK2 kinase inhibitors by CoMFA and CoMSIA methods

Three-dimensional quantitative structure–activity relationship (3D-QSAR) modelling was conducted on a series of leucine-rich repeat kinase 2 (LRRK2) antagonists using CoMFA and CoMSIA methods. The data set, which consisted of 37 molecules, was divided into training and test subsets by using a hierarchical clustering method. Both CoMFA and CoMSIA models were derived using a training set on the basis of the common substructure-based alignment. The optimum PLS model built by CoMFA and CoMSIA provided satisfactory statistical results (q² = 0.589 and r² = 0.927 and q² = 0.473 and r² = 0.802, respectively). The external predictive ability of the models was evaluated by using seven compounds. Moreover, an external evaluation set with known experimental data was used to evaluate the external predictive ability of the porposed models. The statistical parameters indicated that CoMFA (after region focusing) has high predictive ability in comparison with standard CoMFA and CoMSIA models. Molecular docking was also performed on the most active compound to investigate the existence of interactions between the most active inhibitor and the LRRK2 receptor. Based on the obtained results and CoMFA contour maps, some features were introduced to provide useful insights for designing novel and potent LRRK2 inhibitors.     

Antimicrobial performance of nanostructured silica–titania sieves loaded with izohidrafural against microbial strains isolated from urinary tract infections

This study aimed to examine the efficiency of novel bioactive nanostructures represented by silica–titania sieves used as carriers for a new antibacterial agent izohidrafural against bacterial strains isolated from nosocomial urinary tract infections, by using biological quantitative assays. Several release trials have been established and compared with MCM-41 in parallel experiments to achieve the optimum release profile. The obtained systems showed that silica–titania sieves loaded with izohidrafural proved to be the most active material against Klebsiella pneumoniae (average minimal inhibitory concentration [MIC] 40.62 μg/mL), desaminase-positive strains (average MIC 2.925 μg/mL), and Proteus mirabilis (average MIC 9.37 μg/mL), the last being reported with the highest growth rate in the urinary tract catheters. In contrast, the nonloaded silica–titanium sieves exhibited the highest antimicrobial activity against the Gram-positive cocci. Izohidrafural exhibited the highest antimicrobial efficiency, superior to the common drug nitrofurantoin against most Escherichia coli strains, with average MIC of 4.68 μg/mL.     

Computer-aided molecular design of (E)-N-Aryl-2-ethene-sulfonamide analogues as microtubule targeted agents in prostate cancer

Microtubules are tube-shaped, filamentous and cytoskeletal proteins that are essential in all eukaryotic cells. Microtubule is an attractive and promising target for anticancer agents. In this study, three-dimensional quantitative structure activity relationships (3D-QSAR) including comparative molecular field analysis, CoMFA, and comparative molecular similarity indices analysis, CoMSIA, were performed on a set of 45 (E)-N-Aryl-2-ethene-sulfonamide analogues as microtubule-targeted anti-prostate cancer agents. Automated grid potential analysis, AutoGPA module in Molecular Operating Environment 2009.10 (MOE) as a new 3D-QSAR approach with the pharmacophore-based alignment was carried out on the same dataset. AutoGPA-based 3D-QSAR model yielded better prediction parameters than CoMFA and CoMSIA. Based on the contour maps generated from the models, some key features were identified in (E)-N-Aryl-2-arylethene-sulfonamide analogues that were responsible for the anti-cancer activity. Virtual screening was performed based on pharmacophore modeling and molecular docking to identify the new inhibitors from ZINC database. Seven top ranked compounds were found based on Gold score fitness function. In silico ADMET studies were performed on compounds retrieved from virtual screening in compliance with the standard ranges.     

Studies on a Series of Coumarin Derivatives for Anticancer Activity against Breast Carcinoma Cell Line MCF-7 and Their Molecular Design

Breast cancer is one of the most common malignant tumors in women, and is also the focus of researchers. In this article, 3D-QSAR(three-dimensional quantitative structure-activity relationship) was performed on 24 molecules which are a series of coumarin derivatives for their anticancer activity. Our team divided these compounds randomly into the training and test sets to build the CoMFA(comparative molecular field analysis) and CoMSIA(comparative molecular similarity index analysis) models. The coefficients of cross-validation Q~2 and non cross-validation R~2 for CoMFA model were 0.684 and 0.949, and 0.579 and 0.930 for the CoMSIA model, respectively. The result demonstrates that the model has strong stability and satisfactory predictability. 3D contour maps suggest that the electrostatic factor has the greatest impact on activity followed by the H-bonding acceptor and hydrophilic factors. Taking the above results into account, we designed several molecules with high anticancer activity against breast carcinoma cell line MCF-7.     

Synthetic modifications in ethyl 2-amino-4-methylthiazole-5-carboxylate: 3D QSAR analysis and antimicrobial study

Ethyl 2-amino-4-methylthiazole-5-carboxylate (1) is a very substantial derivative of the thiazole group. This derivative has been modified and has been synthesized using readily available materials. The structures of synthesized derivatives were confirmed by IR, ¹H NMR, ¹³C NMR, and mass spectral techniques. The newly prepared compounds (5a–k) were studied for their antimicrobial activities against strains of bacteria (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pyogenes) and fungi (Candida albicans, Aspergillus niger, and Aspergillus clavatus) using serial dilution method. Structure-activity relationship was carried out by CoMFA and CoMSIA with the help of 3D-QSAR analysis. As per the database alignment, the CoMFA and CoMSIA models were developed. Information based on these models is useful for structure-activity relationships of the reported molecules.     

Bioactive polyketides from the sea fan-derived fungus Penicillium citrinum PSU-F51

Five new polyketides including two benzopyranones (1 and 2), one isochroman (3) and two anthraquinone-citrinin derivatives (4 and 5) were isolated from the sea fan-derived fungus Penicillium citrinum PSU-F51 together with thirteen known compounds. The structures were determined by spectroscopic methods. The anthraquinone-citrinin derivatives are rare natural products. Compound 4 displayed moderate antibacterial activity against both Staphylococcus aureus and methicillin-resistant S. aureus with equal MIC values of 16 μg/mL, while the known coniochaetone A displayed moderate antifungal activity against Candida albicans with MIC value of 16 μg/mL.     

QSAR and 3D-QSAR studies of the diacyl-hydrazine derivatives containing furan rings based on the density functional theory

QSAR studies of 27 diacyl-hydrazine derivatives containing furan rings were conducted and compared with the DFT method and AM1-MOPAC method. q ² values of 0.61 and 0.40 validated the predictability and reliability of eq. (5) from the DFT method were higher than those of eq. (6) from the AM1-MOPAC method. The DFT-optimized conformations and ESP-fitting charges of the target compounds were also used for 3D-QSAR analysis, including CoMFA and CoMSIA. The leave-one-out cross-validation correlation coefficient and the good correlation between the predicted and experimental activities of excluded test compounds revealed that CoMFA and CoMSIA models were robust. The QSAR results were consistent with the 3D-QSAR results, indicating that the electrostatic and hydrophobic properties of the target compounds were significant to the biological activity. These models are useful tools for predicting the larvicidal activities of new compounds and designing new specific insect growth regulators.     

Homology modeling and 3D–QSAR study of benzhydrylpiperazine δ opioid receptor agonists

The binding affinity of a series of benzhydrylpiperazine δ opioid receptor agonists were pooled and evaluated by using 3D-QSAR and homology modeling/molecular docking methods. Ligand-based CoMFA and CoMSIA 3D-QSAR analyses with 46 compounds were performed on benzhydrylpiperazine analogues by taking the most active compound BW373U86 as the template. The models were generated successfully with q² value of 0.508 and r² value of 0.964 for CoMFA, and q² value of 0.530 and r² value of 0.927 for CoMSIA. The predictive capabilities of the two models were validated on the test set with R²_pred value of 0.720 and 0.814, respectively. The CoMSIA model appeared to work better in this case. A homology model of active form of δ opioid receptor was established by Swiss-Model using a reported crystal structure of active μ opioid receptor as a template, and was further optimized using nanosecond scale molecular dynamics simulation. The most active compound BW373U86 was docked to the active site of δ opioid receptor and the lowest energy binding pose was then used to identify binding residues such as s Gln105, Lys108, Leu125, Asp128, Tyr129, Leu200, Met132, Met199, Lys214, Trp274, Ile277, Ile304 and Tyr308. The docking and 3D-QSAR results showed that hydrogen bond and hydrophobic interactions played major roles in ligand-receptor interactions. Our results highlight that an approach combining structure-based homology modeling/molecular docking and ligand-based 3D-QSAR methods could be useful in designing of new opioid receptor agonists.     

Design,synthesis of new novel quinoxalin-2(1H)-one derivatives incorporating hydrazone,hydrazine, and pyrazole moieties as antimicrobial potential with in-silico ADME and molecular docking simulation

A series of 6-(morpholinosulfonyl)quinoxalin-2(1H)-one based hydrazone, hydrazine, and pyrazole moieties were designed, synthesized, and evaluated for their in vitro antimicrobial activity. All the synthesized quinoxaline derivatives were characterized by IR, NMR (¹H /¹³C), and EI MS. The results displayed good to moderate antimicrobial potential against six bacterial, and two fungal standard strains. Among the tested derivatives, six quinoxalin-2(1H)-one derivatives 4a, 7, 8a, 11b, 13, and 16 exhibited a significant antibacterial activity with MIC values (0.97–62.5 µg/mL), and MBC values (1.94–88.8 µg/mL) compared with Tetracycline (MICs = 15.62–62.5 µg/mL, and MBCs = 18.74–93.75 µg/mL), and Amphotericin B (MICs = 12.49–88.8 µg/mL, and MFC = 34.62–65.62 µg/mL). In addition, according to CLSI standards, the most active quinoxalin-2(1H)-one derivatives demonstrated bactericidal and fungicidal behavior. Moreover, the most active quinoxaline derivatives showed a considerable antibacterial activity with bactericidal potential against multi-drug resistance bacteria (MDRB) strains with MIC values ranged between (1.95–15.62 µg/mL), and MBC values (3.31–31.25 µg/mL) near to standard Norfloxacin (MIC = 0.78–3.13 µg/mL, and MBC = 1.4–5.32 µg/mL. Further, in vitro S. aureus DNA gyrase inhibition activity were evaluated for the promising derivatives and displayed potency with IC₅₀ values (10.93 ± 1.81–26.18 ± 1.22 µM) compared with Ciprofloxacin (26.31 ± 1.64 µM). Interestingly, these derivatives revealed as good immunomodulatory agents by a percentage ranging between 82.8 ± 0.37 and 142.4 ± 0.98 %. Finally, some in silico ADME, toxicity prediction, and molecular docking simulation were performed and showed a promising safety profile with good binding mode.     

Modiolin and phthalide derivatives from the endophytic fungus Microsphaeropsis arundinis PSU-G18

One new modiolin, microsphaerodiolin (1), and seven new phthalides, microsphaerophthalides A-G (2-8), together with 12 known compounds were isolated from the endophytic fungus Microsphaeropsis arundinis PSU-G18. Their structures were elucidated by spectroscopic methods. The new 3-oxygenated phthalides are rare natural products. The known 1-(2,5-dihydroxyphenyl)-2-buten-1-one exhibited significant antifungal activity against Microsporum gypseum SH-MU-4 with an MIC value of 8 μg/mL, moderate antimalarial activity with an IC₅₀ value of 9.63 μg/mL and strong radical scavenging potency with the IC₅₀ value of 0.018 mg/mL. The new compounds 2 and 6 showed moderately antifungal activity against M. gypseum SH-MU-4 and Cryptococcus neoformans, respectively, with equal MIC values of 64 μg/mL.     

含呋喃环双酰脲类衍生物的三维定量构效关系研究

采用比较分子力场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA), 对27个新型双酰基脲类化合物的杀蚊幼虫(Aedes aegypti L.)活性进行三维定量构效关系(3D-QSAR)研究. 在CoMFA研究中, 考察了网格点步长对统计结果的影响. 在CoMSIA研究中, 系统考察了各种分子场组合、网格点步长和衰减因子对模型统计结果的影响, 发现立体场和氢键供体场的组合得到最佳模型. 所建立的CoMFA和CoMSIA模型的非交叉验证相关系数r2值分别为0.828和0.841, 并都具有较强的预测能力. CoMFA和CoMSIA模型的三维等值图不仅直观地解释了结构与活性的关系, 而且为后续优化该系列化合物提供了理论依据.