Synthesis of xanthone derivatives with extended pi-systems as alpha-glucosidase inhibitors: insight into the probable binding mode

A series of novel xanthone derivatives with extended pi-systems, that is, benzoxanthones 2-4, and their structurally perturbed analogs 5-9 have been designed and synthesized as alpha-glucosidase inhibitors. Their inhibitory activities toward yeast's alpha-glucosidase were evaluated with the aim to enrich the structure-activity relationship. The results indicated that benzoxanthones 2-4 were capable of inhibiting in vitro yeast's alpha-glucosidase 17- to 28-fold more strongly than xanthone derivative 1 that has smaller conjugated pi-system. Benzoxanthone 8, bearing angularly fused aromatic rings, and reduced benzoxanthone 5 showed decreased activities, strongly suggesting that linearly conjugated pi-systems play a crucial role in the inhibition process. O-Methylation of 3-OH of benzoxanthone 2 and nitration at C4 position led to a large decrease in the activity. This indicates that 3-OH of benzoxanthone was crucial to the inhibitory activity, primarily as an H-bonding donor. The present results suggest that pi-pi stacking effect and H-bonding make substantial contributions to elicit the inhibitory activities of this general class of inhibitors.     

A combination of pharmacophore modeling,atom-based 3D-QSAR,molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors

Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC₅₀ ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R^2?=?.9949), cross validation coefficient (Q^2?=?.7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R² value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU–ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.     

Homology modeling and QSAR analysis of 1,3,4-thiadiazole and 1,3,4-triazole derivatives as carbonic anhydrase inhibitors

Carbonic anhydrase (CA) inhibitors are very interesting target for designing anticancer (hypoxic) and antiglaucoma drugs. In the present study, a 3D homology modeling of human carbonic anhydrase-IX (hCA-IX) isozyme, based upon the crystal structure of murine CA-XIVA (PDB CODE 1RJ5) was performed, as no experimental 3D structures are available. A homology model of hCA-IX was developed and validated. To explore the responsible physicochemical properties of 1,3,4-thiadiazole and 1,3,4-triazole derivatives for carbonic anhydrase inhibition, a quantitative structure activity relationship (QSAR) study was performed having hCA-II and hCA-IX inhibitory activity respectively. In hCA-II and hCA-IX inhibitory activities, four significant models with good correlations (> or = 0.945 & > or = 0.926) were obtained; two models (models 1 and 3) were selected based on statistical criterion. The QSAR study revealed that in case of hCA-II, overall increase in size and volume of molecule, introduction of electropositive surfaces might increase the inhibitory activity, whereas in case of hCA-IX, decreasing the hydrophobicity and introduction of electron releasing substituents might increase the hCA-IX inhibitory activity.     

Synthesis of 3-acyloxyxanthone derivatives as α-glucosidase inhibitors: A further insight into the 3-substituents’ effect

Considerable interest has been attracted in xanthone and its derivatives because of their important biological activities. In this paper, a series of novel 3-arylacyloxyxanthone derivatives 2a–p were synthesized and evaluated for their biological activities toward α-glucosidase. In comparison to the parent 1,3-dihydroxylxanthone 1a, 3-arylacyloxy derivatives 2a–p with additional aromatic ester groups at 3-position show up to 13.7-fold higher inhibitory activities. In particular, the IC₅₀ values of compounds 2i, 2m, 2p reach 13.3, 10.6, 11.6 μM, respectively. These results suggest that addition of aromatic moieties by esterification at the 3-OH of the parent 1,3-dihydroxylxanthone is an efficient way to increase the inhibition against α-glucosidase. Different from previous multi-hydroxylxanthones, these 3-arylacyloxyxanthone derivatives show efficient inhibitory activities may due to the π-stacking or hydrophobic effects of the additional aromatic moieties rather than the H-bonding donor interaction of 3-OH. Structure–activity relationship analysis shows that the substituents on the additional aromatic ring also influence the inhibition. All the oxygen or nitrogen-containing groups, like hydroxyl, methoxy, methaminyl, and alkylsilyloxy, can enhance the inhibitory activities. In addition, the kinetics of enzyme inhibition measured by using Lineweaver–Burk plots shows that selected compounds 2i, 2m and 2p are non-competitive inhibitors. Docking simulations further support our structure–activity relationship analysis that additional aromatic moieties enhance inhibitory activities via hydrophobic effects. The new developed 3-arylacyloxyxanthone derivatives probably bind with α-glucosidase in an allosteric site different from traditional multi-hydroxylxanthones.     

Pharmacophore generation and atom-based 3D-QSAR of novel quinoline-3-carbonitrile derivatives as Tpl2 kinase inhibitors

Tumour progression locus-2 (Tpl2) is a serine/threonine kinase, which regulates the expression of tumour necrosis factor α. The article describes the development of a robust pharmacophore model and the investigation of structure-activity relationship analysis of quinoline-3-carbonitrile derivatives reported for Tpl2 kinase inhibition. A five point pharmacophore model (ADRRR) was developed and used to derive a predictive atom-based 3-dimensional quantitative structure activity relationship (3D-QSAR) model. The obtained 3D-QSAR model has an excellent correlation coefficient value (r(2)= 0.96), Fisher ratio (F = 131.9) and exhibited good predictive power (q(2) = 0.79). The QSAR model suggests that the inclusion of hydrophobic substituents will enhance the Tpl2 kinase inhibition. In addition, H-bond donating groups, negative ionic groups and electron withdrawing groups positively contribute to the Tpl2 kinase inhibition. Further, pharmacophoric model was validated by the receiver operating characteristic curve analysis and was employed for virtual screening to identify six potential Tpl2 kinase inhibitors. The findings of this study provide a set of guidelines for designing compounds with better Tpl2 kinase inhibitory potency.     

Synthesis,crystal structure and biological evaluation of new phosphoramide derivatives as urease inhibitors using docking,QSAR and kinetic studies

In an attempt to achieve a new class of phosphoramide inhibitors with high potency and resistance to the hydrolysis process against urease enzyme, we synthesized a series of bisphosphoramide derivatives (01–43) and characterized them by various spectroscopic techniques. The crystal structures of compounds 22 and 26 were investigated using X-ray crystallography. The inhibitory activities of the compounds were evaluated against the jack bean urease and were compared to monophosphoramide derivatives and other known standard inhibitors. The compounds containing aromatic amines and their substituted derivatives exhibited very high inhibitory activity in the range of IC₅₀ = 3.4–1.91 × 10⁻¹⁰ nM compared with monophosphoramides, thiourea, and acetohydroxamic acid. It was also found that derivatives with PO functional groups have higher anti-urease activity than those with PS functional groups. Kinetics and docking studies were carried out to explore the binding mechanism that showed these compounds follow a mixed-type mechanism and, due to their extended structures, can cover the entire binding pocket of the enzyme, reducing the formation of the enzyme-substrate complex. The quantitative structure-activity relationship (QSAR) analysis also revealed that the interaction between the enzyme and inhibitor is significantly influenced by aromatic rings and PO functional groups. Collectively, the data obtained from experimental and theoretical studies indicated that these compounds can be developed as appropriate candidates for urease inhibitors in this field.     

QSAR studies on structurally similar 2-(4-methanesulfonylphenyl)pyran-4-ones as selective COX-2 inhibitors: a Hansch approach

QSAR analysis based on classical Hansch approach was adopted on two recently reported novel series of 2-phenylpyran-4-ones as selective cyclooxygenase-2 (COX-2) inhibitors. The 6-methyl derivatives of title compounds bifurcate as 3-phenoxypyran-4-ones (subset A) and 3-phenylpyran-4-ones (subset B) among series 1. Series 2 consists of 5-chloro derivatives of title compounds. Various regression equations were derived to study the influence of phenoxy and phenyl ring substituents of series 1 compounds on COX-2, COX-1 and selective COX-2 over COX-1 inhibitory activity. The best triparametric equation derived for 36 compounds of series 1 explains the hydrophobic, electronic and steric requirements for improved COX-2 inhibitory activity. QSAR model derived to explore the selective COX-2 over COX-1 inhibition showed that selectivity could be influenced by size and lipophilicity of substituents. The size of the first atom of 2 substituents appears to have negative effect on selectivity, whereas highly polar 3 substituents at R are favorable for improved selectivity. QSAR investigations on series 2 compounds revealed some interesting correlation of COX-2 inhibitory activity with calculated physicochemical properties of whole molecules. The positive logP confirms the hydrophobic interaction of series 2 compounds with COX-2 enzyme. The positive MR term indicates that an overall increase in size and polarizabilty of the molecules increases COX-2 inhibitory activity. The positive contribution of structural variable suggests biphenyl analogs are extremely potent COX-2 inhibitors.     

3D-QSAR and molecular recognition of Klebsiella pneumoniae NDM-1 inhibitors

New Delhi metallo-β-lactamase-1 (NDM-1) as a target for the development of anti-superbug agents, plays an important role in the resistance of β-lactam antibiotics and has received worldwide attention. Sulfhydryl propionic acid derivatives can effectively inhibit the catalytic activity of NDM-1, but the quantitative structure–activity relationship (QSAR) and inhibitor-target recognition mechanism both remain unclear. In this work, CoMFA and CoMSIA models of sulfhydryl propionic acid inhibitors with high predictive ability were obtained, from which the effect of different substituents on the inhibitory activity against NDM-1 were revealed at the molecular level. Then, two 120-nanosecond comparative molecular dynamics (MD) simulations for NDM-1 enzyme and NDM-1-inhibitor complex systems were performed to study the recognition and inhibition mechanism of sulfhydryl propionic acid derivatives. The binding of inhibitors alters the entire H-bond network of the NDM-1 system accompanied by the formation of strong interactions with I35, W93, H120, H122, D124, H189 and H250, further weakens the recognition of NDM-1 by its endogenic substrates. Finally, the results of free energy landscape and conformation cluster analyses show that NDM-1 underwent a significant conformational change after the association with sulfhydryl propionic acid inhibitors. Our findings can provide theoretical support and help for anti-superbug agents design based on the structures of NDM-1 and sulfhydryl propionic acid derivatives.     

Pharmacophore generation and atom-based 3D-QSAR of novel quinoline-3-carbonitrile derivatives as Tpl2 kinase inhibitors

Tumour progression locus-2 (Tpl2) is a serine/threonine kinase, which regulates the expression of tumour necrosis factor α. The article describes the development of a robust pharmacophore model and the investigation of structure-activity relationship analysis of quinoline-3-carbonitrile derivatives reported for Tpl2 kinase inhibition. A five point pharmacophore model (ADRRR) was developed and used to derive a predictive atom-based 3-dimensional quantitative structure activity relationship (3D-QSAR) model. The obtained 3D-QSAR model has an excellent correlation coefficient value (r²?=?0.96), Fisher ratio (F?=?131.9) and exhibited good predictive power (q²?=?0.79). The QSAR model suggests that the inclusion of hydrophobic substituents will enhance the Tpl2 kinase inhibition. In addition, H-bond donating groups, negative ionic groups and electron withdrawing groups positively contribute to the Tpl2 kinase inhibition. Further, pharmacophoric model was validated by the receiver operating characteristic curve analysis and was employed for virtual screening to identify six potential Tpl2 kinase inhibitors. The findings of this study provide a set of guidelines for designing compounds with better Tpl2 kinase inhibitory potency.     

Prediction of HIV-1 protease inhibitory activity of 4-hydroxy-5,6-dihydropyran-2-ones: QSAR study

Inhibition of human immunodeficiency virus 1 (HIV-1) protease is an important strategy for the treatment of HIV and acquired immune deficiency syndrome (AIDS). Therefore, HIV-1 protease inhibitory activity of dihydropyranone derivatives has been analyzed with different physico-chemical parameters. In the present work, QSAR studies were performed on a series of 4-hydroxy-5,6-dihydropyran-2-ones to explore the physico-chemical parameters responsible for their HIV-1 protease inhibitory activity. Physico-chemical parameters were calculated using WIN CAChe 6.1. Stepwise multiple linear regression analysis was performed to derive QSAR models which were further evaluated for statistical significance and predictive power by internal and external validation. The selected best QSAR model was having correlation coefficient (R)?=?0.875 and cross-validated squared correlation coefficient (Q²)?=?0.707. The developed significant QSAR model indicates that hydrophobicity of whole molecule and the substituent present at sixth position of dihydropyranones play an important role in the HIV-1 protease inhibitory activities of 4-hydroxy-5,6-dihydropyran-2-ones.     

芳香羧酸衍生物驱避剂的非线性定量构效关系

【目的】驱避剂可使害虫不敢接近受用者从而保护受用者免遭其害。建立高精度、可解释性强的非线性定量构效关系(quantitative structure activity relationship, QSAR)模型对设计合成新的高效昆虫驱避剂有重要意义。【方法】基于37个芳香羧酸类化合物对家蝇Musca domestica的驱避活性,以量子化学计算软件PCLIENT获取每一化合物初始描述符,以二元矩阵重排过滤器、多轮末尾淘汰实施特征非线性筛选,以支持向量回归(support vector regression, SVR)建立非线性QSAR模型,以SVR非线性解释体系分析各保留描述符对驱避活性的影响。【结果】1 542个初始描述符的SVR模型F=1.2,特征筛选后6个保留描述符的SVR模型F=184.6,特征筛选对QSAR模型精度有重要影响。6个保留分子描述符的重要性依次为p4BCD>GATS7v>T(O..O)> JGI8>SssO>nArCONR2。【结论】保留描述符与芳香羧酸类化合物对家蝇驱避活性的非线性关系明显,获得了高精度、普适性强的非线性SVR-QSAR模型。     

Synthesis, screening and quantitative structure-activity relationship (QSAR) studies of some glutamine analogues for possible anticancer activity

We described the syntheses, biological activities and QSAR studies of 36 new 5-n-substituted-2-(substituted benzenesulphonyl) glutamines 6-41 with different substitutions. These compounds were designed as structural analogues of most reactive amino acid, 'glutamine' (GLN), especially in the tumor cells. They present the new basic lateral chains at R(5) position as well as different substitutions at 2', 3', 4', and 5' positions on the benzene ring. The synthesized compounds have been tested for antitumor activity against Ehrlich ascites carcinoma (EAC) in Swiss albino mice using percentage inhibition of tumor weight as inhibitory parameter. In order to elucidate the structural requirements for antitumor activity, quantitative structure-activity relationship (QSAR) studies have been performed using extra thermodynamic model of Hansch. QSAR equations showed that the electronic parameter (sigma) on the aromatic ring system, steric parameter (Es) and to some extent Sterimol length of the substituent (L) on the aliphatic side chain correlate significantly with the antitumor activity. Resonance factor occupies the major electronic contribution on the aromatic ring system to the activity.     

A quantitative structure–antifungal activity relationship study of oxygenated aromatic essential oil compounds using data structuring and PLS regression analysis

Twenty two oxygenated aromatic essential oil compounds were chosen for the study of the antifungal activity against two wood-decaying fungi, the white-rot Trametes versicolor, which mainly metabolizes lignin, and the brown-rot Coniophoha puteana, which digests cellulose in plant cell walls. Minimal inhibitory concentrations (MICs) were determined by the agar dilution method, using dimethyl sulfoxide (DMSO) as the solvent for the selected compounds and potato-dextrose agar (PDA) as the growth medium for both fungi. The MICs were then used to generate a tree structure, which represents the structuring of the essential oil compounds by the nature and position of the substituents in their aromatic rings, and as dependent variables (log(1/MIC)) in the QSAR analysis. Data structuring proved that a relationship between the molecular structures of the essential oil compounds and their antifungal activity exists, and the hypotheses derived therefrom were complemented by performing a QSAR analysis using the partial least squares (PLS) method. Statistically significant PLS models were obtained with the 1-octanol–water partition coefficient (C log P), the energy of the highest occupied molecular orbital (E _HOMO), and the number of hydrogen-bond donor atoms in the molecules of the compounds studied (Donor) for T. versicolor and with C log P and the fractional negative surface area (FNSA1) for C. puteana.Figure Tree structure representing the structuring of the oxygenated aromatic essential-oil compounds by the position and nature of their substituents in the aromatic ring     

Identification of novel urease inhibitors: pharmacophore modeling,virtual screening and molecular docking studies

Abstract

Pharmacophore modeling and atom-based three-dimensional quantitative structure–activity relationship (3D-QSAR) have been developed on N-acylglycino- and hippurohydroxamic acid derivatives, which are known potential inhibitors of urease. This is followed by virtual screening and ADMET (absorption, distribution, metabolism, excretion and toxicity) studies on a large library of known drugs in order to get lead molecules as Helicobacter pylori urease inhibitors. A suitable three-featured pharmacophore model comprising one H-bond acceptor and two H-bond donor features (ADD.10) has been found to be the best QSAR model. An external library of compounds (～3000 molecules), pre-filtered using Lipinski’s rule of five, has been further screened using the pharmacophore model ADD.10. By analyzing the fitness of the hits with respect to the pharmacophore model and their binding interaction inside the urease active site, four molecules have been predicted to be extremely good urease inhibitors. Two of these have significant potential and should be taken up for further drug-designing process.     

Polyamines and the NMDA receptor: modifying intrinsic activities with aromatic substituents

Thirty-four spermidine (SPD) and spermine (SPM) derivatives with aromatic substituents were synthesized and tested as inhibitors of specific binding of the NMDA channel blocker [3H]MK-801 to membranes prepared from rat hippocampus and cerebral cortex. SPD and SPM derivatives with aromatic substituents at the primary amino groups were the most potent inhibitors (IC50 3.9-4.7 microM). These compounds most likely act directly at the NMDA ion channel, since 30 microM SPM had no pronounced influence on their inhibiting activities. SPD derivatives with aromatic substituents at the secondary amino group were either inactive or highly SPM-sensitive inhibitors (IC50 10-82 microM), depending on the size of the substituent. Our results support the hypothesis that an aromatic interaction site near the center of polyamine derivatives contributes to polyamine inverse agonism.