Dataset Information

Estimation of Inhibitory Effect against Tyrosinase Activity through Homology Modeling and Molecular Docking.

ABSTRACT: Tyrosinase is a key enzyme in melanogenesis. Generally, mushroom tyrosinase from A. bisporus had been used as a model in skin-whitening agent tests employed in the cosmetic industry. The recently obtained crystal structure of bacterial tyrosinase from B. megaterium has high similarity (33.5%) to the human enzyme and thus it was used as a template for constructing of the human model. Binding of tyrosinase to a series of its inhibitors was simulated by automated docking calculations. Docking and MD simulation results suggested that N81, N260, H263, and M280 are involved in the binding of inhibitors to mushroom tyrosinase. E195 and H208 are important residues in bacterial tyrosinase, while E230, S245, N249, H252, V262, and S265 bind to inhibitors and are important in forming pi interaction in human tyrosinase.

SUBMITTER: Nokinsee D

PROVIDER: S-EPMC4693013 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Estimation of Inhibitory Effect against Tyrosinase Activity through Homology Modeling and Molecular Docking.

Nokinsee Daungkamon D Shank Lalida L Lee Vannajan Sanghiran VS Nimmanpipug Piyarat P

Enzyme research 20151215

Tyrosinase is a key enzyme in melanogenesis. Generally, mushroom tyrosinase from A. bisporus had been used as a model in skin-whitening agent tests employed in the cosmetic industry. The recently obtained crystal structure of bacterial tyrosinase from B. megaterium has high similarity (33.5%) to the human enzyme and thus it was used as a template for constructing of the human model. Binding of tyrosinase to a series of its inhibitors was simulated by automated docking calculations. Docking and M ...[more]

PMID: 26788364

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Project description:The ABCB1 transporter also known as P-glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette super-family of transporters; it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping the compounds out of cells. P-gp contributes to a decrease of toxicity and possesses broad substrate specificity. It is involved in the failure of numerous anticancer and antiviral chemotherapies due to the multidrug resistance (MDR) phenomenon, where it removes the chemotherapeutics out of the targeted cells. Understanding the details of the ligand-P-gp interaction is therefore crucial for the development of drugs that might overcome the MRD phenomenon and for obtaining a more effective prediction of the toxicity of certain compounds. In this work, an in silico modeling was performed using homology modeling and molecular docking methods with the aim of better understanding the ligand-P-gp interactions. Based on different mouse P-gp structural templates from the PDB repository, a 3D model of the human P-gp (hP-gp) was constructed by means of protein homology modeling. The homology model was then used to perform molecular docking calculations on a set of thirteen compounds, including some well-known compounds that interact with P-gp as substrates, inhibitors, or both. The sum of ranking differences (SRD) was employed for the comparison of the different scoring functions used in the docking calculations. A consensus-ranking scheme was employed for the selection of the top-ranked pose for each docked ligand. The docking results showed that a high number of π interactions, mainly π-sigma, π-alkyl, and π-π type of interactions, together with the simultaneous presence of hydrogen bond interactions contribute to the stability of the ligand-protein complex in the binding site. It was also observed that some interacting residues in hP-gp are the same when compared to those observed in a co-crystallized ligand (PBDE-100) with mouse P-gp (PDB ID: 4XWK). Our in silico approach is consistent with available experimental results regarding P-gp efflux transport assay; therefore it could be useful in the prediction of the role of new compounds in systemic toxicity.

Project description:This article describes the inhibitory effects of extracts from 25 plants harvested in Sri Lanka against tyrosinase and collagenase. Inhibitors of these enzymes are common ingredients in cosmetics and medications, which help protect the skin against hyperpigmentation and premature aging. The article also discusses the polyphenol content of the extracts, which is well known to possess antioxidant properties. The extract data from the following plants, which have a long history in Sri Lankan traditional medicine, such as Ayurveda, have been provided: English name, "local name in Sri Lanka," (scientific name). Indian copperleaf plant, "kuppameniya," (Acalypha indica); red sandalwood, "madatiya", (Adenanthera pavonina); balipoovu plant, "polpala," (Aerva lanata); snap ginger, "heen araththa," (Alpinia calcarata); bael fruit, "beli," (Aegle marmelos); coastal waterhyssop, "lunuwila," (Bacopa monnieri); porcupine flower, "katu karandu," (Barleria prionitis); balloon-vine plant, "wel penera," (Cardiospermum halicacabum); water caltrop, "Katupila," (Flueggea leucopyrus); Indian sarsparilla, "iramusu," (Hemidesmus indicus); malabar nut plant, "adhatoda," (Justicia adhatoda); wood apple, "divul," (Limonia acidissima); holy basil plant, "maduruthala," (Ocimum tenuiflorum); emblic myrobalan plant, "nelli," (Phyllanthus emblica); long pepper plant,"thippili," (Piper longum); country borage plant, "kapparawalliya," (Plectranthus amboinicus); common sesban, "wel murunga," (Sesbania sesban); turkey berry, "gona batu," (Solanum rudepannum Dunal); purple fruited pea eggplant,"welthibbatu," (Solanum trilobatum); black plum, "madan," (Syzygium cumini); crape jasmine, "wathusudda," (Tabernaemontana divaricate); purple tephrosia, "pila," (Tephrosia purpurea); Chinese chaste tree, "nika," (Vitex negundo); and arctic snow, "suduidda," (Wrightia antidysenterica). The inhibitory effects of these plant extracts on tyrosinase and collagenase, as well as polyphenol contents in the extracts, are detailed in Table 1.

Dataset Information

Estimation of Inhibitory Effect against Tyrosinase Activity through Homology Modeling and Molecular Docking.

Publications

Estimation of Inhibitory Effect against Tyrosinase Activity through Homology Modeling and Molecular Docking.

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