Molecular docking and P-glycoprotein inhibitory activity of Flavonoids
Flavonoids are the most common group of phenolic compounds that have anti-carcinogenic properties and are the constituents of fruits, vegetables and plant derived beverages. In the present study, Flavonoids were docked to three-dimensional structure of P-glycoprotein which plays an important role in...
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| Veröffentlicht in: | Interdisciplinary sciences : computational life sciences 2014-09, Vol.6 (3), p.167-175 |
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| creator | Daddam, Jayasimha Rayalu Dowlathabad, Muralidhara Rao Panthangi, Seshapani Jasti, Pramodakumari |
| description | Flavonoids are the most common group of phenolic compounds that have anti-carcinogenic properties and are the constituents of fruits, vegetables and plant derived beverages. In the present study, Flavonoids were docked to three-dimensional structure of P-glycoprotein which plays an important role in multi drug resistance. A three-dimensional homology model of human P-glycoprotein was built, based on the crystal structure of the 3G5U (Chain A; Structure of a bacterial multidrug ABC transporter) by using Modeller7v7 software. Homology modelling provided a good quality model of the corresponding region in human P-glycoprotein. With the aid of the molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and verify 3D graph programs, which showed that the final refined model is reliable. With this model, a flexible docking study of P-glycoprotein with a group of Flavonoids which were selected from the previous publications was performed. The results indicated THR37, ALA42, ARG40 and ARG47 in P-glycoprotein are important determinant residues in binding as they have strong hydrogen bonding with Flavonoids. These hydrogen binding interactions play an important role for stability of the complex. Among the 10 Flavonoids docked, BiochaninA showed best docking result with P-glycoprotein. Our results may be helpful for further experimental investigations. |
| doi_str_mv | 10.1007/s12539-012-0197-7 |
| format | Article |
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In the present study, Flavonoids were docked to three-dimensional structure of P-glycoprotein which plays an important role in multi drug resistance. A three-dimensional homology model of human P-glycoprotein was built, based on the crystal structure of the 3G5U (Chain A; Structure of a bacterial multidrug ABC transporter) by using Modeller7v7 software. Homology modelling provided a good quality model of the corresponding region in human P-glycoprotein. With the aid of the molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and verify 3D graph programs, which showed that the final refined model is reliable. With this model, a flexible docking study of P-glycoprotein with a group of Flavonoids which were selected from the previous publications was performed. The results indicated THR37, ALA42, ARG40 and ARG47 in P-glycoprotein are important determinant residues in binding as they have strong hydrogen bonding with Flavonoids. These hydrogen binding interactions play an important role for stability of the complex. Among the 10 Flavonoids docked, BiochaninA showed best docking result with P-glycoprotein. Our results may be helpful for further experimental investigations.</description><identifier>ISSN: 1913-2751</identifier><identifier>EISSN: 1867-1462</identifier><identifier>DOI: 10.1007/s12539-012-0197-7</identifier><identifier>PMID: 25205494</identifier><language>eng</language><publisher>Quebec: International Association of Scientists in the Interdisciplinary Areas</publisher><subject>Amino Acid Sequence ; ATP-Binding Cassette, Sub-Family B, Member 1 - chemistry ; Bacteria ; Binding ; Binding Sites ; Biomedical and Life Sciences ; Computational Biology/Bioinformatics ; Computational Science and Engineering ; Computer Appl. in Life Sciences ; Docking ; Drug resistance ; Flavonoids ; Flavonoids - chemistry ; Health Sciences ; Homology ; Human ; Humans ; Life Sciences ; Mathematical and Computational Physics ; Medicine ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Molecular structure ; Phenols ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, Protein ; Software ; Statistics for Life Sciences ; Theoretical ; Theoretical and Computational Chemistry ; Three dimensional</subject><ispartof>Interdisciplinary sciences : computational life sciences, 2014-09, Vol.6 (3), p.167-175</ispartof><rights>International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2014</rights><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-b390fd367531df03dcaed85c4e18463fce5edc4a2ecf4969e7c5ed6d42db28873</citedby><cites>FETCH-LOGICAL-c405t-b390fd367531df03dcaed85c4e18463fce5edc4a2ecf4969e7c5ed6d42db28873</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12539-012-0197-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12539-012-0197-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51298</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25205494$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Daddam, Jayasimha Rayalu</creatorcontrib><creatorcontrib>Dowlathabad, Muralidhara Rao</creatorcontrib><creatorcontrib>Panthangi, Seshapani</creatorcontrib><creatorcontrib>Jasti, Pramodakumari</creatorcontrib><title>Molecular docking and P-glycoprotein inhibitory activity of Flavonoids</title><title>Interdisciplinary sciences : computational life sciences</title><addtitle>Interdiscip Sci Comput Life Sci</addtitle><addtitle>Interdiscip Sci</addtitle><description>Flavonoids are the most common group of phenolic compounds that have anti-carcinogenic properties and are the constituents of fruits, vegetables and plant derived beverages. In the present study, Flavonoids were docked to three-dimensional structure of P-glycoprotein which plays an important role in multi drug resistance. A three-dimensional homology model of human P-glycoprotein was built, based on the crystal structure of the 3G5U (Chain A; Structure of a bacterial multidrug ABC transporter) by using Modeller7v7 software. Homology modelling provided a good quality model of the corresponding region in human P-glycoprotein. With the aid of the molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and verify 3D graph programs, which showed that the final refined model is reliable. With this model, a flexible docking study of P-glycoprotein with a group of Flavonoids which were selected from the previous publications was performed. The results indicated THR37, ALA42, ARG40 and ARG47 in P-glycoprotein are important determinant residues in binding as they have strong hydrogen bonding with Flavonoids. These hydrogen binding interactions play an important role for stability of the complex. Among the 10 Flavonoids docked, BiochaninA showed best docking result with P-glycoprotein. Our results may be helpful for further experimental investigations.</description><subject>Amino Acid Sequence</subject><subject>ATP-Binding Cassette, Sub-Family B, Member 1 - chemistry</subject><subject>Bacteria</subject><subject>Binding</subject><subject>Binding Sites</subject><subject>Biomedical and Life Sciences</subject><subject>Computational Biology/Bioinformatics</subject><subject>Computational Science and Engineering</subject><subject>Computer Appl. in Life Sciences</subject><subject>Docking</subject><subject>Drug resistance</subject><subject>Flavonoids</subject><subject>Flavonoids - chemistry</subject><subject>Health Sciences</subject><subject>Homology</subject><subject>Human</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Mathematical and Computational Physics</subject><subject>Medicine</subject><subject>Models, Molecular</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular Sequence Data</subject><subject>Molecular 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The results indicated THR37, ALA42, ARG40 and ARG47 in P-glycoprotein are important determinant residues in binding as they have strong hydrogen bonding with Flavonoids. These hydrogen binding interactions play an important role for stability of the complex. Among the 10 Flavonoids docked, BiochaninA showed best docking result with P-glycoprotein. Our results may be helpful for further experimental investigations.</abstract><cop>Quebec</cop><pub>International Association of Scientists in the Interdisciplinary Areas</pub><pmid>25205494</pmid><doi>10.1007/s12539-012-0197-7</doi><tpages>9</tpages></addata></record> |
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| subjects | Amino Acid Sequence ATP-Binding Cassette, Sub-Family B, Member 1 - chemistry Bacteria Binding Binding Sites Biomedical and Life Sciences Computational Biology/Bioinformatics Computational Science and Engineering Computer Appl. in Life Sciences Docking Drug resistance Flavonoids Flavonoids - chemistry Health Sciences Homology Human Humans Life Sciences Mathematical and Computational Physics Medicine Models, Molecular Molecular Dynamics Simulation Molecular Sequence Data Molecular structure Phenols Protein Structure, Tertiary Sequence Alignment Sequence Analysis, Protein Software Statistics for Life Sciences Theoretical Theoretical and Computational Chemistry Three dimensional |
| title | Molecular docking and P-glycoprotein inhibitory activity of Flavonoids |
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