Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors
<p>Proper docking protocols were presented for three known enzyme structures, human betasecretase (BACE1), Aromatase and pyruvate dehydogenase kinase (PDHK) using Autodock4.2 and Vina softwares. The validity of docking protocols was verified using a set of known active ligands and decoys for a...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Shiraz University of Medical Sciences
2017-03-01
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| Series: | Trends in Pharmaceutical Sciences |
| Online Access: | http://tips.sums.ac.ir/index.php/TiPS/article/view/116 |
| _version_ | 1798044336845225984 |
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| author | Zahra Rezaei Masood Fereidoonnezhad Zeinab Faghih Hossein Sadeghpur Ayyub Mojaddami Amirhossein Sakhteman |
| author_facet | Zahra Rezaei Masood Fereidoonnezhad Zeinab Faghih Hossein Sadeghpur Ayyub Mojaddami Amirhossein Sakhteman |
| author_sort | Zahra Rezaei |
| collection | DOAJ |
| description | <p>Proper docking protocols were presented for three known enzyme structures, human betasecretase (BACE1), Aromatase and pyruvate dehydogenase kinase (PDHK) using Autodock4.2 and Vina softwares. The validity of docking protocols was verified using a set of known active ligands and decoys for all three enzymes. Different energy minimization algorithms were performed prior to docking of each ligand in order to find out by which method a more reasonable correlation between binding energy and corresponding experimental activity of the compounds was obtained. The highest ROC<sub>AUC</sub> value was 0.916, 0.914 and 0. 833 when MM<sup>+</sup>-PM3 methods were applied as minimization method, whereas without minimization it was 0.127, 0.187, and 0.51 for PDHK, BACE-1 and aromatase, respectively. So a combination of molecular mechanics (MM<sup>+</sup>) and a semi-empirical method (PM3 or AM1) could promote the docking protocol in case of all targets. Protein ligand interaction studies using self-organizing map (SOM) were also conducted in order to reveal the validity of docking protocol and to evaluate its predictive ability in terms of distinguishing between ligands and decoys. <strong></strong></p> |
| first_indexed | 2024-04-11T23:02:13Z |
| format | Article |
| id | doaj.art-ecc25d57f94d4752b4116eded17e745f |
| institution | Directory Open Access Journal |
| issn | 2423-3722 2423-5652 |
| language | English |
| last_indexed | 2024-04-11T23:02:13Z |
| publishDate | 2017-03-01 |
| publisher | Shiraz University of Medical Sciences |
| record_format | Article |
| series | Trends in Pharmaceutical Sciences |
| spelling | doaj.art-ecc25d57f94d4752b4116eded17e745f2022-12-22T03:58:07ZengShiraz University of Medical SciencesTrends in Pharmaceutical Sciences2423-37222423-56522017-03-0131314210.1111/tips.v3i1.11680Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitorsZahra Rezaei0Masood FereidoonnezhadZeinab FaghihHossein SadeghpurAyyub MojaddamiAmirhossein SakhtemanDepartment of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.<p>Proper docking protocols were presented for three known enzyme structures, human betasecretase (BACE1), Aromatase and pyruvate dehydogenase kinase (PDHK) using Autodock4.2 and Vina softwares. The validity of docking protocols was verified using a set of known active ligands and decoys for all three enzymes. Different energy minimization algorithms were performed prior to docking of each ligand in order to find out by which method a more reasonable correlation between binding energy and corresponding experimental activity of the compounds was obtained. The highest ROC<sub>AUC</sub> value was 0.916, 0.914 and 0. 833 when MM<sup>+</sup>-PM3 methods were applied as minimization method, whereas without minimization it was 0.127, 0.187, and 0.51 for PDHK, BACE-1 and aromatase, respectively. So a combination of molecular mechanics (MM<sup>+</sup>) and a semi-empirical method (PM3 or AM1) could promote the docking protocol in case of all targets. Protein ligand interaction studies using self-organizing map (SOM) were also conducted in order to reveal the validity of docking protocol and to evaluate its predictive ability in terms of distinguishing between ligands and decoys. <strong></strong></p>http://tips.sums.ac.ir/index.php/TiPS/article/view/116 |
| spellingShingle | Zahra Rezaei Masood Fereidoonnezhad Zeinab Faghih Hossein Sadeghpur Ayyub Mojaddami Amirhossein Sakhteman Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors Trends in Pharmaceutical Sciences |
| title | Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors |
| title_full | Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors |
| title_fullStr | Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors |
| title_full_unstemmed | Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors |
| title_short | Comparison of docking procedures and its efficiency for Betasecretase, Aromatase and Pyruvate dehydrogenase kinase inhibitors |
| title_sort | comparison of docking procedures and its efficiency for betasecretase aromatase and pyruvate dehydrogenase kinase inhibitors |
| url | http://tips.sums.ac.ir/index.php/TiPS/article/view/116 |
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