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ABSTRACT: Polo-box domain 1 (PBD1) is a characteristic domain of polo-like kinase 1 (PLK1), which locates in C-terminal and can influence the catalytic activity and specific subcellular locations of PLK1. At present, most PLK1 inhibitors are developed to occupy the ATP pocket or its close sites. However, this kind of PLK1 inhibitors is difficult to pursue target selectivity and may encounter cross drug resistance with other kinase inhibitors due to the conserved sequence of ATP pocket. Recently, PBD1, with aberrant specificity in sequence and structure, has attracted enormous interests as the alternative target to the discovery of corresponding inhibitors for anti-tumor drugs. The structure and function of PBD1 as well as the advances of its inhibitors are reviewed in this paper.
Yao xue xue bao = Acta pharmaceutica Sinica 03/2013; 48(3):315-24.
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Yanmin Zhang,
Haichun Liu,
Yu Jiao,
Haoliang Yuan,
Fengxiao Wang,
Shuai Lu,
Sihui Yao,
Zhipeng Ke,
Wenting Tai,
Yulei Jiang,
Yadong Chen, Tao Lu
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ABSTRACT: Vascular endothelial growth factor (VEGF) and its receptor tyrosine kinase VEGFR-2 or kinase insert domain receptor (KDR) have been identified as promising targets for novel anticancer agents. To achieve new potent inhibitors of KDR, we conducted molecular fragment replacement (MFR) studies for the understanding of 3D-QSAR modeling and the docking investigation of arylphthalazines and 2-((1H-Azol-1-yl)methyl)-N-arylbenzamides-based KDR inhibitors. Two favorable 3D-QSAR models (CoMFA with q (2), 0.671; r (2), 0.969; CoMSIA with q (2), 0.608; r (2), 0.936) have been developed to predict the biological activity of new compounds. The new molecular database generated by MFR was virtually screened using Glide (docking) and further evaluated with CoMFA prediction, protein-ligand interaction fingerprint (PLIF) and ADMET analysis. 44 N-(pyridin-4-ylmethyl)aniline derivatives as novel potential KDR inhibitors were finally obtained. In this paper, the work flow developed could be applied to de novo drug design and virtual screening potential KDR inhibitors, and use hit compounds to further optimize and design new potential KDR inhibitors.
Molecular Diversity 10/2012; · 3.15 Impact Factor
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ABSTRACT: A series of diaryl ether hydroxamic acids were synthesized for the first time and evaluated for the HDAC biology and antiproliferative activity. The structures of these new hydroxamic acids derivatives were confirmed by IR, (1)H-NMR and mass spectrum. Some of these compounds showed micro molar activity in the HDAC inhibitory assay and against four cancer cell lines.
Archives of Pharmacal Research 10/2012; 35(10):1723-32. · 1.59 Impact Factor
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ABSTRACT: β-Carboline family of compounds is a large group of alkaloids widely distributed in nature and exhibits broad-spectrum anti-tumor activities. We designed and synthesized two series of novel 1-carboxamide- and 6-sulfonamide-substituted β-carboline derivatives 7a-p and 12a-b, and their wild type B-Raf kinase inhibitory activities were described. Most compounds showed moderate to excellent inhibitory activities. Among them, 1-carboxamide-6-(N-(3-(dimethylamino)propyl)-sulfamoyl)-β-carboline, 7e exhibited potent activity (IC(50)=1.62 μM), showing the potential for further investigation as a lead compound.
Bioorganic & medicinal chemistry letters 05/2012; 22(14):4783-6. · 2.65 Impact Factor
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ABSTRACT: Polo-like kinase 1 is an important and attractive oncological target that plays a key role in mitosis and cytokinesis. A combined pharmacophore- and docking-based virtual screening was performed to identify novel polo-like kinase 1 inhibitors. A total of 34 hit compounds were selected and tested in vitro, and some compounds showed inhibition of polo-like kinase 1 and human tumor cell growth. The most potent compound (66) inhibited polo-like kinase 1 with an IC(50) value of 6.99 μm. The docked binding models of two hit compounds were discussed in detail. These compounds contained novel chemical scaffolds and may be used as foundations for the development of novel classes of polo-like kinase 1 inhibitors.
Chemical Biology & Drug Design 05/2012; 80(2):328-39. · 2.28 Impact Factor
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ABSTRACT: Mesenchymal epithelial transition factor (c-Met) is an attractive target for cancer therapy. Three-dimensional pharmacophore hypotheses were built based on a set of known structurally diverse c-Met inhibitors. The best pharmacophore model, which identified inhibitors with an associated correlation coefficient of 0.983 between their experimental and estimated IC(50) values, consisted of two hydrogen-bond acceptors, one hydrophobic, and one ring aromatic feature. The highly predictive power of the model was rigorously validated by test set prediction and Fischer's randomization method. The high values of enrichment factor and receiver operating characteristic (ROC) score indicated the model performed fairly well at distinguishing active from inactive compounds. The model was then applied to screen compound database for potential c-Met inhibitors. A filtering protocol, including druggability and molecular docking, were also applied in hits selection. The final 38 molecules, which exhibited good estimated activities, desired binding mode and favorable drug likeness were identified as potential c-Met inhibitors. Their novel backbone structures could be served as scaffolds for further study, which may facilitate the discovery and rational design of potent c-Met kinase inhibitors.
Journal of Molecular Modeling 12/2011; 18(7):3087-100. · 1.80 Impact Factor
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Jian Wang,
Ya-Dong Chen,
Hai-Chun Liu,
Guo-Wu Lin,
Tao-Tao Yang,
Hao-Liang Yuan,
Ting Ran,
Shuai Lu,
Wei-Wei Zhang,
Ying Leng, Tao Lu
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ABSTRACT: Cyclin-dependent kinase 2 (CDK2) has appeared as an important drug target over the years with a multitude of therapeutic potentials. To design compounds with enhanced inhibitory potencies against CDK2, 3D-QSAR and molecular fragment replacement studies were performed on the pyrazolo[4,3-h]quinazoline derivatives, a class of potent CDK2 inhibitors. The contours of 3D-QSAR model revealed important structural features of the inhibitors related to the active site of CDK2. Based on the pyrazolo[4,3-h]quinazoline core, the different substituents at three important points were replaced with diverse molecular fragments. The compounds resulting from fragments assembly with pyrazolo[4,3-h]quinazoline core were then scored with the robust 3D-QSAR model. Furthermore, the absorption, distribution, metabolism and excretion properties of these compounds were predicted by Volsurf to eliminate inappropriate compounds. Thirty-one new potential compounds were finally obtained. These results initiated us to further optimise and design new potential inhibitors.
Molecular Simulation 09/2011; 37(10):824-836. · 1.33 Impact Factor
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ABSTRACT: The phosphatidylinositol-3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) signaling pathway plays a critical role in the regulation of cellular growth, survival and proliferation. mTOR and PI3K have attracted particular attention as cancer targets. These kinases belong to the phosphatidylinositol-3-kinase-related kinase (PIKK) family and therefore have considerable homology in their active sites. To accelerate the discovery of inhibitors with selective activity against mTOR and PI3K as cancer targets, in this work, a homology model of mTOR was developed to identify the structural divergence in the active sites between mTOR and PI3Kα. Furthermore, two highly predictive comparative molecular similarity index analyses (CoMSIA) models were built based on 304 selective inhibitors docked into mTOR and PI3Kα, respectively (mTOR: q(2) = 0.658, r(pre)(2) = 0.839; PI3Kα: q(2) = 0.540, r(pre)(2) = 0.719). The results showed that steric and electrostatic fields have an important influence on selectivity towards mTOR and PI3Kα-a finding consistent with the structural divergence between the active sites. The findings may be helpful in investigating selective mTOR/PI3Kα inhibitors.
Journal of Molecular Modeling 04/2011; 18(1):171-86. · 1.80 Impact Factor
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ABSTRACT: Fragment-based drug design (FBDD) is considered a promising approach in lead discovery. However, for a practical application of this approach, problems remain to be solved. Hence, a novel practical strategy for three-dimensional lead discovery is presented in this work. Diverse fragments with spatial positions and orientations retained in separately adjacent regions were generated by deconstructing well-aligned known inhibitors in the same target active site. These three-dimensional fragments retained their original binding modes in the process of new molecule construction by fragment linking and merging. Root-mean-square deviation (rmsd) values were used to evaluate the conformational changes of the component fragments in the final compounds and to identify the potential leads as the main criteria. Furthermore, the successful validation of our strategy is presented on the basis of two relevant tumor targets (CDK2 and c-Met), demonstrating the potential of our strategy to facilitate lead discovery against some drug targets.
Journal of Chemical Information and Modeling 03/2011; 51(4):959-74. · 4.68 Impact Factor
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ABSTRACT: Polo-like kinase 1, an important enzyme with diverse biological actions in cell mitosis, is a promising target for developing novel anticancer drugs. A combined molecular docking, structure-based pharmacophore modeling and three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a set of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as PLK1 inhibitors. The common substructure, molecular docking and pharmacophore-based alignment were used to develop different 3D-QSAR models. The comparative molecular field analysis (CoMFA) and comparative molecule similarity indices analysis (CoMSIA) models gave statistically significant results. These models showed good q(2) and r(2) (pred) values and revealed a good response to test set validation. All of the structural insights obtained from the 3D-QSAR contour maps are consistent with the available crystal structure of PLK1. The contour maps obtained from the 3D-QSAR models in combination with the structure based pharmacophore model help to better interpret the structure-activity relationship. These satisfactory results may aid the design of novel PLK1 inhibitors. This is the first report on 3D-QSAR study of PLK1 inhibitors.
International Journal of Molecular Sciences 01/2011; 12(12):8713-39. · 2.60 Impact Factor
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Phosphorus Sulfur and Silicon and the Related Elements 01/2011; Sulfur(and Silicon and the Related Elements):189-204. · 0.72 Impact Factor
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ABSTRACT: A mild and efficient two-step synthesis of 3-substituted beta-carbolinone derivatives from 3-substituted beta-carboline in good yields is described. A possible reaction mechanism for the formation of the skeleton of beta-carbolin-1-one is proposed. The structures of these compounds were established by IR, 1H-NMR, 13C-NMR, mass spectrometry and elemental analysis, as well as X-ray crystallographic analysis of 4-2 and 6-2.
Molecules 08/2010; 15(8):5680-91. · 2.39 Impact Factor
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ABSTRACT: Oncogenic B-Raf has been identified in a variety of cancers with high incidence, especially in malignant melanoma and thyroid cancer. Most B-Raf mutations elicit elevated kinase activity and the constitutive activation of Ras/Raf/MEK/ERK pathway, which induces proliferation and promotes malignant transformation. Therefore, B-Raf inhibitors, targeting B-Raf or mutated B-Raf, have received increasing momentum in oncology drug discovery arena. This review focuses on the diverse small-molecule inhibitors of B-Raf kinase recently reported in the literature, including those currently in clinical and preclinical phase. They are described as two categories, type I or type II kinase inhibitors, based on their different mechanism of action with active or inactive conformations of the B-Raf kinase derived from the available crystal structures or molecular docking analysis. A particular emphasis is placed on their binding modes and the structure-activity relationship (SAR) of each chemical structure class.
Current Medicinal Chemistry 05/2010; 17(16):1618-1634. · 4.86 Impact Factor
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ABSTRACT: Oncogenic B-Raf has been identified in a variety of cancers with high incidence, especially in malignant melanoma and thyroid cancer. Most B-Raf mutations elicit elevated kinase activity and the constitutive activation of Ras/Raf/MEK/ERK pathway, which induces proliferation and promotes malignant transformation. Therefore, B-Raf inhibitors, targeting B-Raf or mutated B-Raf, have received increasing momentum in oncology drug discovery arena. This review focuses on the diverse small-molecule inhibitors of B-Raf kinase recently reported in the literature, including those currently in clinical and preclinical phase. They are described as two categories, type I or type II kinase inhibitors, based on their different mechanism of action with active or inactive conformations of the B-Raf kinase derived from the available crystal structures or molecular docking analysis. A particular emphasis is placed on their binding modes and the structure-activity relationship (SAR) of each chemical structure class.
Current Medicinal Chemistry 03/2010; 17(16):1618-34. · 4.86 Impact Factor
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ABSTRACT: A three dimensional (3D) chemical feature based pharmacophore model was developed for selective histone deacetylase 1 (HDAC1) inhibitors, which provides an efficient way to discuss the isoform selectivity of HDAC inhibitors. In contrast to the classical pan-HDAC pharmacophore, two hydrophobic features (HY and HYAr2) were found in the chemical feature based pharmacophore model, which might be responsible for the selectivity of HDAC1 inhibitions. Molecular docking also highlighted the two hydrophobic features, which are located in the internal cavity adjacent to the active site. The results contribute to our understanding of the molecular mechanism underlying the selectivity of HDAC1 inhibitors and suggest a possible target region to design novel selective HDAC1 inhibitors.
European journal of medicinal chemistry 01/2010; 45(5):1777-91. · 3.27 Impact Factor
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ABSTRACT: In the title compound, [Zn(C(8)H(5)N(2)O(2))(2)(H(2)O)], the Zn(II) ion is coordinated in each case by a carboxyl-ate O atom and an imidazole N atom from two different benzimidazole-2-carboxyl-ate (BIC) ligands and one water O atom in a trigonal-bipyramidal geometry. In the complex mol-ecule, the two benzimidazole planes are twisted, making a dihedral angle of 55.93 (11)°. The three-dimensional framework is organized by inter-molecular N-H⋯O hydrogen bonding and O-H⋯O inter-actions and π-π inter-actions between adjacent benzimidazole rings [centroid-centroid distance = 3.586 (3) Å].
Acta Crystallographica Section E Structure Reports Online 01/2010; 66(Pt 6):m610-1. · 0.35 Impact Factor
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ABSTRACT: Checkpoint kinase 1 (Chk1), a member of the serine/threonine kinase family, is an attractive therapeutic target for anticancer combination therapy. A structure-based modeling approach complemented with shape components was pursued to develop a reliable pharmacophore model for ATP-competitive Chk1 inhibitors. Common chemical features of the pharmacophore model were derived by clustering multiple structure-based pharmacophore features from different Chk1-ligand complexes in comparable binding modes. The final model consisted of one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD), two hydrophobic (HY) features, several excluded volumes and shape constraints. In the validation study, this feature-shape query yielded an enrichment factor of 9.196 and performed fairly well at distinguishing active from inactive compounds, suggesting that the pharmacophore model can serve as a reliable tool for virtual screening to facilitate the discovery of novel Chk1 inhibitors. Besides, these pharmacophore features were assumed to be essential for Chk1 inhibitors, which might be useful for the identification of potential Chk1 inhibitors.
Journal of Molecular Modeling 12/2009; 16(7):1195-204. · 1.80 Impact Factor
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ABSTRACT: Periodic density functional theory calculations are used to systematically investigate, for the first time, the mechanisms for chemical transformations of (R,R)-tartaric acid on a model Cu(110) surface. The overall potential energy surface for the chemical transformations is revealed. The calculations show that the adsorption of the intact biacid molecules of (R,R)-tartaric acid on Cu(110) surface is not strong, but upon adsorption on Cu(110), the biacid molecules will chemically transform immediately, rather than desorb from the surface. It is found that the chemical transformations of (R,R)-tartaric acid on Cu(110) is a thermodynamically favorable process, to produce the monotartrate species, bitartrate species, and H atoms. Kinetically, the initial reaction step is only one O-H bond scission in either one of the COOH group of a biacid molecule of (R,R)-tartaric acid leading to the formation of a monotartrate species and a H atom, which is an almost spontaneous process. The rate-controlling step is the O-H bond scission in the COOH group of a monotartrate species producing a bitartrate species and a H atom. The concerted reaction for simultaneously breaking the two O-H bonds in both COOH groups of a biacid molecule cannot proceed.
The Journal of chemical physics 10/2009; 131(14):144703. · 3.09 Impact Factor
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ABSTRACT: A three-dimensional (3D) quantitative pharmacophore model was developed from a training set of structurally diverse substituted ureas against Raf-1 kinase, which was well validated to be highly predictive by two methods, namely, test set prediction and Cat-Scramble method. Then a virtual database searching was performed with the pharmacophore model as a 3D query, and the bioactivities of the retrieved hits were predicted by the pharmacophore. Subsequently, molecular docking was carried out on the selected hits whose estimated IC(50) was less than 1 microM. Finally, 29 hits were identified as potential leads against Raf-1 kinase, which exhibited good estimated activities, high docking scores, similar binding mode to experimentally proven compounds and favorable drug-like properties. The study may facilitate the discovery and rational design of novel leads with potent inhibitory activity targeting Raf-1 kinase.
European journal of medicinal chemistry 10/2008; 44(3):1240-9. · 3.27 Impact Factor
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ABSTRACT: The title compound, [Co(C(19)H(15)N(3)O(5)S)(C(12)H(8)N(2))] x 5 H(2)O, has a moderately distorted octahedral coordination environment composed of two N atoms of a 1,10-phenanthroline ligand and one N and three O atoms of an N-{[4-(1,3-benzothiazol-2-yl)anilino]carbonylmethyl}iminodiacetate (ZL-5(2-)) ligand. The ring systems of the phenanthroline and ZL-5(2-) ligands are coplanar and the complexes pack in layers parallel to the ab plane with the rings of adjacent complexes facing one another. The layers stack along the c axis and are linked by hydrogen bonds involving the five water solvent molecules in the asymmetric unit and O atoms of the acetate groups of the ZL-5(2-) ligand. This is believed to be the first crystal structure of a complex of a 2-(4-aminophenyl)benzothiazole ligand.
Acta crystallographica. Section C, Crystal structure communications 05/2008; 64(Pt 4):m179-81. · 0.78 Impact Factor
