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      In Silico Identification of Potent Pancreatic Triacylglycerol Lipase Inhibitors from Traditional Chinese Medicine

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      1 , 2 , 2 , 3 , 2 , 3 , 4 , 5 , 6 , *
      PLoS ONE
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          Abstract

          Pancreatic triacylglycerol lipase (PNLIP) are primary lipases that are critical for triacylglyceride digestion in human. Since reduced metabolism of triacylglyceride might be a plausible concept for weight loss, we screened for potential PNLIP inhibitors from traditional Chinese medicine (TCM) with the aim to identify weight loss candidate compounds. TCM candidates Aurantiamide, Cnidiadin, and 2-hexadecenoic acid exhibited higher Dock Scores than the commercial drug Orlistat, and were also predicted to have inhibitory characteristics against PNLIP using constructed MLR (R 2 = 0.8664) and SVM (R 2 = 0.9030) models. Molecular dynamics indicated that the TCM-PNLIP complexes formed were stable. We identified that the PNLIP binding site has several residues that can serve as anchors, and a hydrophobic corridor that provides additional stability to the complex. Aurantiamide, Cnidiadin, and 2-hexadecenoic acid all have features that correspond to these binding site features, indicating their potential as candidates for PNLIP inhibitors. The information presented in this study may provide helpful insights to designing novel weight-control drugs.

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          Most cited references25

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          LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.

          The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. The output is a colour, or black-and-white, PostScript file giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities. The program is completely general for any ligand and can also be used to show other types of interaction in proteins and nucleic acids. It was designed to facilitate the rapid inspection of many enzyme complexes, but has found many other applications.
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            TCM Database@Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico

            Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine.
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              Structure of human pancreatic lipase.

              Pancreatic lipase (triacylglycerol acyl hydrolase) fulfills a key function in dietary fat absorption by hydrolysing triglycerides into diglycerides and subsequently into monoglycerides and free fatty acids. We have determined the three-dimensional structure of the human enzyme, a single-chain glycoprotein of 449 amino acids, by X-ray crystallography and established its primary structure by sequencing complementary DNA clones. Enzymatic activity is lost after chemical modification of Ser 152 in the porcine enzyme, indicating that this residue is essential in catalysis, but other data are more consistent with a function in interfacial recognition. Our structural results are evidence that Ser 152 is the nucleophilic residue essential for catalysis. It is located in the larger N-terminal domain at the C-terminal edge of a doubly wound parallel beta-sheet and is part of an Asp-His-Ser triad, which is chemically analogous to, but structurally different from, that in the serine proteases. This putative hydrolytic site is covered by a surface loop and is therefore inaccessible to solvent. Interfacial activation, a characteristic property of lipolytic enzymes acting on water-insoluble substrates at water-lipid interfaces, probably involves a reorientation of this flap, not only in pancreatic lipases but also in the homologous hepatic and lipoprotein lipases.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                6 September 2012
                : 7
                : 9
                : e43932
                Affiliations
                [1 ]Department of Chinese Medicine, China Medical University, Taichung, Taiwan
                [2 ]Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
                [3 ]Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
                [4 ]Department of Biotechnology, Asia University, Taichung, Taiwan
                [5 ]Department of Biomedical Informatics, Asia University, Taichung, Taiwan
                [6 ]China Medical University Beigang Hospital, Yunlin, Taiwan
                Consiglio Nazionale delle Ricerche, Italy
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: CYCC. Performed the experiments: KYC. Analyzed the data: KYC SC. Contributed reagents/materials/analysis tools: CYCC. Wrote the paper: KYC SC CYCC.

                Article
                PONE-D-12-13205
                10.1371/journal.pone.0043932
                3435334
                22970152
                b1bfff05-630f-470c-9383-5596787535be
                Copyright @ 2012

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 May 2012
                : 27 July 2012
                Page count
                Pages: 11
                Funding
                The research was supported by grants from the National Science Council of Taiwan (NSC 100-2325-B-039-001), Committee on Chinese Medicine and Pharmacy (CCMP100-RD-030), China Medical University and Asia University (DMR-101-094). This study is also supported in part by Taiwan Department of Health Clinical Trial and Research Center of Excellence (DOH101-TD-B-111-004) and Taiwan Department of Health Cancer Research Center of Excellence (DOH101-TD-C-111-005). Partial funding is also provided by China Medical University Beigang Hospital (CMUBH R101-004). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Biophysics
                Biomacromolecule-Ligand Interactions
                Biophysics Simulations
                Chemistry
                Computational Chemistry
                Molecular Dynamics
                Molecular Mechanics
                Computer Science
                Computer Applications
                Computer-Aided Design
                Computer Modeling
                Medicine
                Drugs and Devices
                Drug Research and Development
                Drug Discovery
                Nutrition
                Obesity

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                Uncategorized

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