<strong>Objective:</strong><span style="font-family:""><span style="font-family:Verdana;"> Breast cancer is a public health challenge on a global scale that is caused b...<strong>Objective:</strong><span style="font-family:""><span style="font-family:Verdana;"> Breast cancer is a public health challenge on a global scale that is caused by environmental or genetic factors. Breast cancer is affecting both males and females, but there is still a lack of effective drugs with improved potency and admissibility against breast cancer as many of the breast cancer drugs have severe side effects. </span><b><span style="font-family:Verdana;">Methods:</span></b><span style="font-family:Verdana;"> The docking approach has been used </span><span><span style="font-family:Verdana;">to find a new compound for breast cancer with more efficacy and tolerance and with lesser side effects. A ligand-based pharmacophore approach has been generated for 39 anticancer compounds with significance for the development of new drugs. </span><b><span style="font-family:Verdana;">Result:</span></b><span style="font-family:Verdana;"> Through docking, the approach found new lead compoun</span></span><span style="font-family:Verdana;">ds for breast cancer. The proposed pharmacophore model in this study contains two HBAs and one HYD</span></span><span style="font-family:Verdana;">,</span><span style="font-family:""><span style="font-family:Verdana;"> one hydrophobic domain </span><span style="font-family:Verdana;">and</span><span style="font-family:Verdana;"> two Aromatic rings</span></span><span style="font-family:""><span style="font-family:Verdana;"> and the estimated distance range is minimum to maxi</span><span style="font-family:Verdana;">mum of derived pharmacophore features.</span></span><span style="font-family:""> <b><span style="font-family:Verdana;">Conclusion:</span></b><span style="font-family:Verdana;"> Based on this research, it is proposed that these two lead compounds may be able to be used against EGFR in breast cancer. New compounds can be identified based on common features in the Pharmacophore model. 3D pharmacophore triangle could be used for further studies because this pharmacophore has better merging and in the future for more studies can suggest the same distance range of pha</span></span><span style="font-family:Verdana;">rmacophore features as this pharmacophore.</span>展开更多
The aberrant overexpression of cyclin-dependent kinase 9 (CDK9) in cancer cells results in the loss of proliferative control, making it an attractive therapeutic target for various cancers. However, the highly structu...The aberrant overexpression of cyclin-dependent kinase 9 (CDK9) in cancer cells results in the loss of proliferative control, making it an attractive therapeutic target for various cancers. However, the highly structural similarity between CDK9 and CDK2 makes the development of novel selective CDK9 inhibitors a challenging task and thus limits their clinical applications. Here, an effective two-stage virtual screening strategy was developed to identify novel CDK9 inhibitors with better inhibitory activity and higher selectivity. The first screening stage aims to select potential compounds with better inhibitory activity than Roniciclib, one of the most effective CDK9 inhibitors, through reliable structure-based pharmacophoric virtual screening and accurate molecular docking analyses. The second stage employs a very detailed visual inspection process, in which several structural criteria describing the major difference between the binding pockets of CDK9 and CDK2 are taken into consideration, to identify compounds with higher selectivity than CAN508, one of the CDK9 inhibitors with distinguished selectivity. Finally, three compounds (NCI207113 from NCI database and TCM0004 and TCM3282 from TCM database) with better inhibitory activity and higher selectivity were successfully identified as novel CDK9 inhibitors. These three compounds also display excellent binding stabilities, great pharmacokinetic properties and low toxicity in MD simulations and ADMET predictions. Besides, the results of binding free energy calculations suggest that enhancing van der Waals interaction and nonpolar solvation energy and/or reducing polar solvation energy can significantly improve the binding affinity of these CDK9 inhibitors. Their clinical potentials to serve as anticancer drug candidates can be further evaluated through a series of <em>in vitro/in vivo</em> bioassays in the future. To the best of our knowledge, this is the first attempt to identify novel CDK9 inhibitors with both better inhibitory activity and higher selectivity through an effective two-stage virtual screening strategy.展开更多
3-Arylisothiazolo[5,4-b]quinolin-4(9H)-ones and 3-arylisoxazolo[5,4-b]quinolin-4(9H)-ones were synthesized and assayed for affinity for the benzodiazepine binding site of the GABAA receptors. While the 3-arylisothiazo...3-Arylisothiazolo[5,4-b]quinolin-4(9H)-ones and 3-arylisoxazolo[5,4-b]quinolin-4(9H)-ones were synthesized and assayed for affinity for the benzodiazepine binding site of the GABAA receptors. While the 3-arylisothiazoloquinolin-4-ones were found to be potent ligands, with affinities (expressed as the affinity Ki value) down to 1 nM, the 3-arylisoxazoloquinolin-4-ones are less potent. This is suggested to depend on sterical repulsive interaction of the 3-arylisoxazoloquinolin-4-ones with the receptor essential volume of the binding site, and a higher electron density at the nitrogen in the azole ring (N-2) as well as the carbonyl oxygen in the isothiazoloquinolin-4-ones enabling them to interact stronger with hydrogen bond donor sites at the binding site.展开更多
28 kinds of carotenoids are studied to reveal the key parameters and regulation on the singlet oxygen quenching rate.First,the quantum chemistry parameters of carotenoids calculated by Gaussian software combined with ...28 kinds of carotenoids are studied to reveal the key parameters and regulation on the singlet oxygen quenching rate.First,the quantum chemistry parameters of carotenoids calculated by Gaussian software combined with substitution parameters were used to construct the quantitative structure-activity relationship model(QSAR)of the singlet oxygen quenching rate of carotenoids.The key parameters affecting the antioxidant activity of carotenoids are revealed,and the data predicted via the QSAR model were provided for subsequent research.Then,a three-dimensional(3D)pharmacophore model was used to regulate and modify the antioxidant activity of carotenoids.The correlation coefficients of the modeling group(R2)and verification group(Rpre2)of the established QSAR model were 0.945 and 0.916,respectively,which can be used for the analysis of antioxidant activity of carotenoids;the antioxidant activity of carotenoids can be significantly regulated by the number of conjugated C=C bonds,the energy difference between frontier molecular orbitals and the partial Mulliken charge in C1 and theπ···π*excitation energy E(s);the antioxidant activity of carotenoids can be effectively regulated by the hydrogen bond acceptor pharmacophores on both sides of the conjugated C=C bonds and the hydrophobic groups on the conjugated C=C bond;the hydrophobic substituents attached to conjugated C=C bonds can effectively improve the singlet oxygen quenching rate of carotenoids.展开更多
Chiral drug naftopidil(NAF), a specific α1D-adrenoceptor(AR) antagonist for the treatment of benign prostatic hyperplasia, was used in racemic form for several decades. Our recent work declared that NAF enantiomers s...Chiral drug naftopidil(NAF), a specific α1D-adrenoceptor(AR) antagonist for the treatment of benign prostatic hyperplasia, was used in racemic form for several decades. Our recent work declared that NAF enantiomers showed the same antagonistic effects on the α1D-AR, but the binding mechanism of these two stereochemical NAF isomers to the α1D receptor remained unclear. Herein, we reported the crystallographic structures of optically pure NAF stereoisomers for the first time and unambiguously determined their absolute configurations. The crystal data of R and S enantiomers matched satisfactorily the pharmacophore model for α1D-selective antagonists. Based on the constructed α1D homology model,molecular docking studies shed light on the molecular mechanism of NAF enantiomers binding to α1D-AR. The results indicated that NAF enantiomers exhibited the very similar binding poses and occupied the same binding pocket.展开更多
Matrix metalloproteinase-13(MMP-13) has been considered as a promising therapeutic target for osteoarthritis. In this work, the experimental crystal structures of five MMP-13-ligand complexes are used to build the mul...Matrix metalloproteinase-13(MMP-13) has been considered as a promising therapeutic target for osteoarthritis. In this work, the experimental crystal structures of five MMP-13-ligand complexes are used to build the multiple structure-based pharmacophore model of MMP-13 inhibitors. The reliability of pharmacophore model is validated using a decoy set. The pharmacophore model contains four chemical features: two hydrogen bond acceptor(HBA), one hydrophobic(HY) feature, and one ring aromatic(RA) feature. Particularly, the HY feature is found to orient the MMP-13 inhibitors deep into the S1’ pocket of MMP-13 to produce selective inhibition. By carrying out the screening of pharmacophore model and subsequent molecular docking, the four non-zinc-chelating selective MMP-13 inhibitors of natural products(NP-015973, NP-000814, STOCK1 N-24933, and STOCK1 N-69443) are identified. It is found that the binding modes of MMP-13 with our screened four natural products are very similar to the reported experimental binding mode of MMP-13 with the most active inhibitor(GG12003, IC50: 0.67 n M), and each of them involves the interactions of a ligand with the three amino acid residues Thr226, Lys119, and His201 of MMP-13 receptor. This shows that our modeling results are in good agreement with the relevant experimental results, which strongly supports our screened MMP-13 inhibitors of natural products. These screened natural products may be used as the lead compounds of MMP-13 inhibitors in the future studies of structural modifications.展开更多
文摘<strong>Objective:</strong><span style="font-family:""><span style="font-family:Verdana;"> Breast cancer is a public health challenge on a global scale that is caused by environmental or genetic factors. Breast cancer is affecting both males and females, but there is still a lack of effective drugs with improved potency and admissibility against breast cancer as many of the breast cancer drugs have severe side effects. </span><b><span style="font-family:Verdana;">Methods:</span></b><span style="font-family:Verdana;"> The docking approach has been used </span><span><span style="font-family:Verdana;">to find a new compound for breast cancer with more efficacy and tolerance and with lesser side effects. A ligand-based pharmacophore approach has been generated for 39 anticancer compounds with significance for the development of new drugs. </span><b><span style="font-family:Verdana;">Result:</span></b><span style="font-family:Verdana;"> Through docking, the approach found new lead compoun</span></span><span style="font-family:Verdana;">ds for breast cancer. The proposed pharmacophore model in this study contains two HBAs and one HYD</span></span><span style="font-family:Verdana;">,</span><span style="font-family:""><span style="font-family:Verdana;"> one hydrophobic domain </span><span style="font-family:Verdana;">and</span><span style="font-family:Verdana;"> two Aromatic rings</span></span><span style="font-family:""><span style="font-family:Verdana;"> and the estimated distance range is minimum to maxi</span><span style="font-family:Verdana;">mum of derived pharmacophore features.</span></span><span style="font-family:""> <b><span style="font-family:Verdana;">Conclusion:</span></b><span style="font-family:Verdana;"> Based on this research, it is proposed that these two lead compounds may be able to be used against EGFR in breast cancer. New compounds can be identified based on common features in the Pharmacophore model. 3D pharmacophore triangle could be used for further studies because this pharmacophore has better merging and in the future for more studies can suggest the same distance range of pha</span></span><span style="font-family:Verdana;">rmacophore features as this pharmacophore.</span>
文摘The aberrant overexpression of cyclin-dependent kinase 9 (CDK9) in cancer cells results in the loss of proliferative control, making it an attractive therapeutic target for various cancers. However, the highly structural similarity between CDK9 and CDK2 makes the development of novel selective CDK9 inhibitors a challenging task and thus limits their clinical applications. Here, an effective two-stage virtual screening strategy was developed to identify novel CDK9 inhibitors with better inhibitory activity and higher selectivity. The first screening stage aims to select potential compounds with better inhibitory activity than Roniciclib, one of the most effective CDK9 inhibitors, through reliable structure-based pharmacophoric virtual screening and accurate molecular docking analyses. The second stage employs a very detailed visual inspection process, in which several structural criteria describing the major difference between the binding pockets of CDK9 and CDK2 are taken into consideration, to identify compounds with higher selectivity than CAN508, one of the CDK9 inhibitors with distinguished selectivity. Finally, three compounds (NCI207113 from NCI database and TCM0004 and TCM3282 from TCM database) with better inhibitory activity and higher selectivity were successfully identified as novel CDK9 inhibitors. These three compounds also display excellent binding stabilities, great pharmacokinetic properties and low toxicity in MD simulations and ADMET predictions. Besides, the results of binding free energy calculations suggest that enhancing van der Waals interaction and nonpolar solvation energy and/or reducing polar solvation energy can significantly improve the binding affinity of these CDK9 inhibitors. Their clinical potentials to serve as anticancer drug candidates can be further evaluated through a series of <em>in vitro/in vivo</em> bioassays in the future. To the best of our knowledge, this is the first attempt to identify novel CDK9 inhibitors with both better inhibitory activity and higher selectivity through an effective two-stage virtual screening strategy.
基金Financial support from the Swedish Board for Scientific Research(VR),the Knut and Alice Wallenberg Foundation,the Research School for Pharmaceutical Sciences at Lund University,Carlsberg Foundation,Denmark,and the NeuroScience PharmaBiotec Research Center,Den-mark,is gratefully acknowledged.
文摘3-Arylisothiazolo[5,4-b]quinolin-4(9H)-ones and 3-arylisoxazolo[5,4-b]quinolin-4(9H)-ones were synthesized and assayed for affinity for the benzodiazepine binding site of the GABAA receptors. While the 3-arylisothiazoloquinolin-4-ones were found to be potent ligands, with affinities (expressed as the affinity Ki value) down to 1 nM, the 3-arylisoxazoloquinolin-4-ones are less potent. This is suggested to depend on sterical repulsive interaction of the 3-arylisoxazoloquinolin-4-ones with the receptor essential volume of the binding site, and a higher electron density at the nitrogen in the azole ring (N-2) as well as the carbonyl oxygen in the isothiazoloquinolin-4-ones enabling them to interact stronger with hydrogen bond donor sites at the binding site.
文摘28 kinds of carotenoids are studied to reveal the key parameters and regulation on the singlet oxygen quenching rate.First,the quantum chemistry parameters of carotenoids calculated by Gaussian software combined with substitution parameters were used to construct the quantitative structure-activity relationship model(QSAR)of the singlet oxygen quenching rate of carotenoids.The key parameters affecting the antioxidant activity of carotenoids are revealed,and the data predicted via the QSAR model were provided for subsequent research.Then,a three-dimensional(3D)pharmacophore model was used to regulate and modify the antioxidant activity of carotenoids.The correlation coefficients of the modeling group(R2)and verification group(Rpre2)of the established QSAR model were 0.945 and 0.916,respectively,which can be used for the analysis of antioxidant activity of carotenoids;the antioxidant activity of carotenoids can be significantly regulated by the number of conjugated C=C bonds,the energy difference between frontier molecular orbitals and the partial Mulliken charge in C1 and theπ···π*excitation energy E(s);the antioxidant activity of carotenoids can be effectively regulated by the hydrogen bond acceptor pharmacophores on both sides of the conjugated C=C bonds and the hydrophobic groups on the conjugated C=C bond;the hydrophobic substituents attached to conjugated C=C bonds can effectively improve the singlet oxygen quenching rate of carotenoids.
基金supported by grants from the National Science Foundation of Guangdong Province (No. S2013040014088)the Postdoctoral Science Foundation of Guangzhou City (Q188)partially supported by the Guangdong Major Scientific and Technological Special Project for New Drug Development (2013A022100029)
文摘Chiral drug naftopidil(NAF), a specific α1D-adrenoceptor(AR) antagonist for the treatment of benign prostatic hyperplasia, was used in racemic form for several decades. Our recent work declared that NAF enantiomers showed the same antagonistic effects on the α1D-AR, but the binding mechanism of these two stereochemical NAF isomers to the α1D receptor remained unclear. Herein, we reported the crystallographic structures of optically pure NAF stereoisomers for the first time and unambiguously determined their absolute configurations. The crystal data of R and S enantiomers matched satisfactorily the pharmacophore model for α1D-selective antagonists. Based on the constructed α1D homology model,molecular docking studies shed light on the molecular mechanism of NAF enantiomers binding to α1D-AR. The results indicated that NAF enantiomers exhibited the very similar binding poses and occupied the same binding pocket.
文摘Matrix metalloproteinase-13(MMP-13) has been considered as a promising therapeutic target for osteoarthritis. In this work, the experimental crystal structures of five MMP-13-ligand complexes are used to build the multiple structure-based pharmacophore model of MMP-13 inhibitors. The reliability of pharmacophore model is validated using a decoy set. The pharmacophore model contains four chemical features: two hydrogen bond acceptor(HBA), one hydrophobic(HY) feature, and one ring aromatic(RA) feature. Particularly, the HY feature is found to orient the MMP-13 inhibitors deep into the S1’ pocket of MMP-13 to produce selective inhibition. By carrying out the screening of pharmacophore model and subsequent molecular docking, the four non-zinc-chelating selective MMP-13 inhibitors of natural products(NP-015973, NP-000814, STOCK1 N-24933, and STOCK1 N-69443) are identified. It is found that the binding modes of MMP-13 with our screened four natural products are very similar to the reported experimental binding mode of MMP-13 with the most active inhibitor(GG12003, IC50: 0.67 n M), and each of them involves the interactions of a ligand with the three amino acid residues Thr226, Lys119, and His201 of MMP-13 receptor. This shows that our modeling results are in good agreement with the relevant experimental results, which strongly supports our screened MMP-13 inhibitors of natural products. These screened natural products may be used as the lead compounds of MMP-13 inhibitors in the future studies of structural modifications.
