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      The effect of Aspalathus linearis (Burm.f.) R.Dahlgren and its compounds on tyrosinase and melanogenesis

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          Abstract

          Pigmentation, a process controlled by melanogenesis, plays a vital role in protecting the skin against harmful ultraviolet rays. The level of protection is compromised in case of hypopigmentation. This study aimed to evaluate an Aspalathus linearis extract, fractions and phytoconstituents, for their efficacy on melanogenesis stimulation. Fifteen compounds were kinetically assessed against tyrosinase; the rate-limiting enzyme of melanogenesis. Aspalathin and catechin significantly ( p value < 0.001) increased the enzymatic rate, showing 50% stimulatory effects at 119.70 ± 2.06 µg/mL and 143.30 ± 2.74 µg/mL, respectively, by acting as subversive substrates. Five compounds inhibited the enzyme’s activity, of which four exhibited competitive inhibition. To investigate the molecular interactions between the compounds and the active site, molecular docking was done, using tyrosinase (PBD: 2Y9X) and tyrosinase related protein 1 (PBD: 5M8P). All the compounds docked successfully with acceptable docking scores. Further quantitative structure–activity relationship analysis identified potential functional groups, linked to the specific activity. The crude extract, its fractions, and compounds exhibited low antiproliferative activity with 50% cell viability at concentrations higher than 100 µg/mL. Finally, both aspalathin and catechin exhibited a significant increase (4.5%) in melanin production at 119.82 µg/mL and 76.92 µg/mL, respectively. This is the first report of A. linearis’ compounds on skin re-pigmentation.

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          Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.

          Structure-based virtual screening plays an important role in drug discovery and complements other screening approaches. In general, protein crystal structures are prepared prior to docking in order to add hydrogen atoms, optimize hydrogen bonds, remove atomic clashes, and perform other operations that are not part of the x-ray crystal structure refinement process. In addition, ligands must be prepared to create 3-dimensional geometries, assign proper bond orders, and generate accessible tautomer and ionization states prior to virtual screening. While the prerequisite for proper system preparation is generally accepted in the field, an extensive study of the preparation steps and their effect on virtual screening enrichments has not been performed. In this work, we systematically explore each of the steps involved in preparing a system for virtual screening. We first explore a large number of parameters using the Glide validation set of 36 crystal structures and 1,000 decoys. We then apply a subset of protocols to the DUD database. We show that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets. We provide examples illustrating the structural changes introduced by the preparation that impact database enrichment. While the work presented here was performed with the Protein Preparation Wizard and Glide, the insights and guidance are expected to be generalizable to structure-based virtual screening with other docking methods.
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            Cancer chemoprevention with dietary phytochemicals.

            Chemoprevention refers to the use of agents to inhibit, reverse or retard tumorigenesis. Numerous phytochemicals derived from edible plants have been reported to interfere with a specific stage of the carcinogenic process. Many mechanisms have been shown to account for the anticarcinogenic actions of dietary constituents, but attention has recently been focused on intracellular-signalling cascades as common molecular targets for various chemopreventive phytochemicals.
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              Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules.

              Epik is a computer program for predicting pK(a) values for drug-like molecules. Epik can use this capability in combination with technology for tautomerization to adjust the protonation state of small drug-like molecules to automatically generate one or more of the most probable forms for use in further molecular modeling studies. Many medicinal chemicals can exchange protons with their environment, resulting in various ionization and tautomeric states, collectively known as protonation states. The protonation state of a drug can affect its solubility and membrane permeability. In modeling, the protonation state of a ligand will also affect which conformations are predicted for the molecule, as well as predictions for binding modes and ligand affinities based upon protein-ligand interactions. Despite the importance of the protonation state, many databases of candidate molecules used in drug development do not store reliable information on the most probable protonation states. Epik is sufficiently rapid and accurate to process large databases of drug-like molecules to provide this information. Several new technologies are employed. Extensions to the well-established Hammett and Taft approaches are used for pK(a) prediction, namely, mesomer standardization, charge cancellation, and charge spreading to make the predicted results reflect the nature of the molecule itself rather just for the particular Lewis structure used on input. In addition, a new iterative technology for generating, ranking and culling the generated protonation states is employed.
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                Author and article information

                Contributors
                analikeblom@gmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                29 March 2021
                29 March 2021
                2021
                : 11
                : 7020
                Affiliations
                [1 ]GRID grid.49697.35, ISNI 0000 0001 2107 2298, Department of Plant and Soil Sciences, , University of Pretoria, ; Pretoria, South Africa
                [2 ]GRID grid.134936.a, ISNI 0000 0001 2162 3504, School of Natural Resources, , University of Missouri, ; Columbia, USA
                [3 ]College of Pharmacy, JSS Academy of Higher Education and Research, Mysore, India
                Author information
                http://orcid.org/0000-0002-0031-1269
                http://orcid.org/0000-0003-0940-8099
                http://orcid.org/0000-0002-3242-3476
                Article
                86410
                10.1038/s41598-021-86410-z
                8007633
                33782442
                c3002948-c8d1-4052-8741-8781072bcd05
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 May 2020
                : 8 February 2021
                Funding
                Funded by: National Research Foundation
                Award ID: Innovation Scholarship
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                cell biology,computational biology and bioinformatics,enzymes,natural products
                Uncategorized
                cell biology, computational biology and bioinformatics, enzymes, natural products

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