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Roxas JDP, San Juan MAD, Villagracia ARC, Espiritu RA. An in silico analysis of the interaction of marine sponge-derived bioactive compounds with type 2 diabetes mellitus targets DPP-4 and PTP1B. J Biomol Struct Dyn 2024:1-14. [PMID: 38189304 DOI: 10.1080/07391102.2024.2301751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Type 2 diabetes is a medical condition involving elevated blood glucose levels resulting from impaired or improper insulin utilization. As the number of type 2 diabetes cases increases each year, there is an urgent need to develop novel drugs having new targets and/or complementing existing therapeutic protocols. In this regard, marine sponge-derived compounds hold great potential due to their potent biological activity and structural diversity. In this study, a small library of 50 marine sponge-derived compounds were examined for their activity towards type 2 diabetes targets, namely dipeptidyl peptidase-4 (DPP-4) and protein tyrosine phosphatase 1B (PTP1B). The compounds were first subjected to molecular docking on protein models based on their respective co-crystal structures to assess binding free energies (BFE) and conformations. Clustering analysis yielded BFE that ranged from 24.54 kcal/mol to -9.97 kcal/mol for DPP-4, and from -4.98 kcal/mol to -8.67 kcal/mol for PTP1B. Interaction analysis on the top ten compounds with the most negative BFE towards each protein target showed similar intermolecular interactions and key interacting residues as in the previously solved co-crystal structure. These compounds were subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling to characterize drug-likeness and combining the results from these analyses, (S)-6'-debromohamacanthin B was identified as a potential multi-target inhibitor of DPP-4 and PTP1B, having favorable protein interaction, no Lipinski violations, good gastrointestinal (GI) tract absorption, blood-brain barrier (BBB) penetration, and no predicted toxicity. Finally, the interaction of (S)-6'-debromohamacanthin B with the two proteins was validated using molecular dynamics simulations over 100 ns through RMSD, radius of gyration, PCA, and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) confirming favorable interactions with the respective proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Al Rey C Villagracia
- Department of Physics, De La Salle University, Manila, Philippines
- Advanced Nanomaterials Investigation and Molecular Simulations (ANIMoS) Research Unit, CENSER, De La Salle University, Manila, Philippines
| | - Rafael A Espiritu
- Department of Chemistry, De La Salle University, Manila, Philippines
- Translational Research and Medicine (TRaM) Research Unit, CENSER, De La Salle University, Manila, Philippines
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A Novel PTP1B Inhibitor-Phosphate of Polymannuronic Acid Ameliorates Insulin Resistance by Regulating IRS-1/Akt Signaling. Int J Mol Sci 2021; 22:ijms222312693. [PMID: 34884501 PMCID: PMC8657924 DOI: 10.3390/ijms222312693] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 02/06/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a critical negative modulator of insulin signaling and has attracted considerable attention in treating type 2 diabetes mellitus (T2DM). Low-molecular-weight polymannuronic acid phosphate (LPMP) was found to be a selective PTP1B inhibitor with an IC50 of 1.02 ± 0.17 μM. Cellular glucose consumption was significantly elevated in insulin-resistant HepG2 cells after LPMP treatment. LPMP could alleviate oxidative stress and endoplasmic reticulum stress, which are associated with the development of insulin resistance. Western blot and polymerase chain reaction (PCR) analysis demonstrated that LPMP could enhance insulin sensitivity through the PTP1B/IRS/Akt transduction pathway. Furthermore, animal study confirmed that LPMP could decrease blood glucose, alleviate insulin resistance, and exert hepatoprotective effects in diabetic mice. Taken together, LPMP can effectively inhibit insulin resistance and has high potential as an anti-diabetic drug candidate to be further developed.
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Zhao J, Xu P, Liu X, Ji X, Li M, Dev S, Qu X, Lu W, Niu B. Application of machine learning methods for the development of antidiabetic drugs. Curr Pharm Des 2021; 28:260-271. [PMID: 34161205 DOI: 10.2174/1381612827666210622104428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/10/2021] [Indexed: 11/22/2022]
Abstract
Diabetes is a chronic non-communicable disease caused by several different routes, which has attracted increasing attention. In order to speed up the development of new selective drugs, machine learning (ML) technology has been applied in the process of diabetes drug development, which opens up a new blueprint for drug design. This review provides a comprehensive portrayal of the application of ML in antidiabetic drug use.
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Affiliation(s)
- Juanjuan Zhao
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Pengcheng Xu
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Xiujuan Liu
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Xiaobo Ji
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Minjie Li
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Sooranna Dev
- Department of Obstetrics and Gynaecology, Imperial College London, Fulham Road, London SW10 9 NH, United Kingdom
| | - Xiaosheng Qu
- National Engineering Laboratory of Southwest Endangered Medicinal Resources Development, Guangxi Botanical Garden of Medicinal Plants, No. 189, Changgang Road, 530023, Nanning, China
| | - Wencong Lu
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Bing Niu
- School of Life Sciences, Shanghai University, 200444, China
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Gao Y, Wang G, Wang X, Yang Y, Niu X. Structure-Activity relationship of MDSA and its derivatives against Staphylococcus aureus Ser/Thr phosphatase Stp1. Comput Biol Chem 2020; 85:107230. [DOI: 10.1016/j.compbiolchem.2020.107230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 01/23/2023]
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Conformation and dynamics of the C-terminal region in human phosphoglycerate mutase 1. Acta Pharmacol Sin 2017; 38:1673-1682. [PMID: 28748916 DOI: 10.1038/aps.2017.37] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/09/2017] [Indexed: 12/24/2022] Open
Abstract
Phosphoglycerate mutase 1 (PGAM1), an important enzyme in glycolysis, is overexpressed in a number of human cancers, thus has been proposed as a promising metabolic target for cancer treatments. The C-terminal portion of the available crystal structures of PGAM1 and its homologous proteins is partially disordered, as evidenced by weak electron density. In this study, we identified the conformational behavior of the C-terminal region of PGAM1 as well as its role during the catalytic cycle. Using the PONDR-FIT server, we demonstrated that the C-terminal region was intrinsically disordered. We applied the Monte Carlo (MC) method to explore the conformational space of the C-terminus and conducted a series of explicit-solvent molecular dynamics (MD) simulations, and revealed that the C-terminal region is inherently dynamic; large-scale conformational changes in the C-terminal segment led to the structural transition of PGAM1 from the closed state to the open state. Furthermore, the C-terminal segment influenced 2,3-bisphosphoglycerate (2,3-BPG) binding. The proposed swing model illustrated a critical role of the C-terminus in the catalytic cycle through the conformational changes. In conclusion, the C-terminal region induces large movements of PGAM1 from the closed state to the open state and influences cofactor binding during the catalytic cycle. This report describes the dynamic features of the C-terminal region in detail and should aid in design of novel and efficient inhibitors of PGAM1. A swing mechanism of the C-terminal region is proposed, to facilitate further studies of the catalytic mechanism and the physiological functions of its homologues.
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Xu Q, Luo J, Wu N, Zhang R, Shi D. BPN, a marine-derived PTP1B inhibitor, activates insulin signaling and improves insulin resistance in C2C12 myotubes. Int J Biol Macromol 2017; 106:379-386. [PMID: 28811203 DOI: 10.1016/j.ijbiomac.2017.08.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/06/2023]
Abstract
Insulin resistance is a key feature of type 2 diabetes mellitus (T2DM) and is characterized by defects in insulin signaling. Protein tyrosine phosphatase 1B (PTP1B) is a major negative regulator of insulin signaling cascade and has attracted intensive investigation in recent T2DM therapy study. BPN, a marine-derived bromophenol compound, was isolated from the red alga Rhodomela confervoides. This study investigated the effects of BPN on the insulin signaling pathway in insulin-resistant C2C12 myotubes by inhibiting PTP1B. Molecular docking study and analysis of small- molecule interaction with PTP1B all showed BPN inhibited PTP1B activity via binding to the catalytic site through hydrogen bonds. We then found that BPN permeated into C2C12 myotubes, on the one hand, activated insulin signaling in an insulin-independent manner in C2C12 cells; on the other hand, ameliorated palmitate-induced insulin resistance through augmenting insulin sensitivity. Moreover, our studies also showed that PTP1B inhibition by BPN increased glucose uptake in normal and insulin-resistant C2C12 myotubes through glucose transporter 4 (GLUT4) translocation. Taken together, BPN activates insulin signaling and alleviates insulin resistance and represents a potential candidate for further development as an antidiabetic agent.
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Affiliation(s)
- Qi Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; The University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiao Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; The University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ning Wu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Renshuai Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dayong Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; The University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Lipchock JM, Hendrickson HP, Douglas BB, Bird KE, Ginther PS, Rivalta I, Ten NS, Batista VS, Loria JP. Characterization of Protein Tyrosine Phosphatase 1B Inhibition by Chlorogenic Acid and Cichoric Acid. Biochemistry 2017; 56:96-106. [PMID: 27959494 PMCID: PMC5292209 DOI: 10.1021/acs.biochem.6b01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a known regulator of the insulin and leptin signaling pathways and is an active target for the design of inhibitors for the treatment of type II diabetes and obesity. Recently, cichoric acid (CHA) and chlorogenic acid (CGA) were predicted by docking methods to be allosteric inhibitors that bind distal to the active site. However, using a combination of steady-state inhibition kinetics, solution nuclear magnetic resonance experiments, and molecular dynamics simulations, we show that CHA is a competitive inhibitor that binds in the active site of PTP1B. CGA, while a noncompetitive inhibitor, binds in the second aryl phosphate binding site, rather than the predicted benzfuran binding pocket. The molecular dynamics simulations of the apo enzyme and cysteine-phosphoryl intermediate states with and without bound CGA suggest CGA binding inhibits PTP1B by altering hydrogen bonding patterns at the active site. This study provides a mechanistic understanding of the allosteric inhibition of PTP1B.
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Affiliation(s)
- James M. Lipchock
- Department of Chemistry, Washington College, Chestertown, Maryland 21620, United States
| | - Heidi P. Hendrickson
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Bonnie B. Douglas
- Department of Chemistry, Washington College, Chestertown, Maryland 21620, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Kelly E. Bird
- Department of Chemistry, Washington College, Chestertown, Maryland 21620, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Patrick S. Ginther
- Department of Chemistry, Washington College, Chestertown, Maryland 21620, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Ivan Rivalta
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Univ Lyon, Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Nicholas S. Ten
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
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Guan SS, Han WW, Zhang H, Wang S, Shan YM. Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation. J Biomol Struct Dyn 2015; 34:15-28. [PMID: 25582663 DOI: 10.1080/07391102.2015.1007167] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Angiotensin-converting enzyme (ACE), a membrane-bound zinc metallopeptidase, catalyzes the formation of Angiotensin-II (AngII) and the deactivation of bradykinin in the renin-angiotensin-aldosterone and kallikrein-kinin systems. As a hydrolysis product of ACE, AngII is regarded as an inhibitor and displays stronger competitive inhibition in the C-domain than the N-domain of ACE. However, the AngII binding differences between the two domains and the mechanisms behind AngII dissociation from the C-domain are rarely explored. In this work, molecular docking, Molecular Mechanics/Poisson-Boltzmann Surface Area calculation, and steered molecular dynamics (SMD) are applied to explore the structures and interactions in the binding or unbinding of AngII with the two domains of human somatic ACE. Calculated free energy values suggest that the C-domain-AngII complex is more stable than the N-domain-AngII complex, consistent with available experimental data. SMD simulation results imply that electrostatic interaction is dominant in the dissociation of AngII from the C-domain. Moreover, Gln106, Asp121, Glu123, and Tyr213 may be the key residues in the unbinding pathway of AngII. The simulation results in our work provide insights into the interactions between the two domains of ACE and its natural peptide inhibitor AngII at a molecular level. Moreover, the results provide theoretical clues for the design of new inhibitors.
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Affiliation(s)
- Shan-shan Guan
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Wei-wei Han
- b Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , School of Life Sciences, Jilin University , Changchun 130023 , People's Republic of China
| | - Hao Zhang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Song Wang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Ya-ming Shan
- c School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China
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9
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Kocakaya SO. The Molecular Modeling of Novel Inhibitors of Protein Tyrosine Phosphatase 1B Based on Catechol by MD and MM-GB (PB)/SA Calculations. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.6.1769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Yang L, Tang Z, Liu W, Xiao J, Hu S, Yang L, Liu W, Deng H, Feng Q. Evolutional and functional analysis of a serine protease in Spodoptera litura. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2012; 81:121-135. [PMID: 22930521 DOI: 10.1002/arch.21049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Spodoptera litura is a threatening agricultural insect in tropical and subtropical areas and accounts for tremendous annual crop losses. As seen in virtually all insect species, serine proteases (SPs) are crucial to S. litura. The expression pattern of SPs from the midgut of S. litura was studied through expressed sequence tags (ESTs) analysis. One of SP (SlSP1) was chosen for detailed study, because the expression of the gene was midgut and larvae specific. SlSP1 was conducted as a model of its evolution, structure, and potential binding activity with corresponding substrates. SlSP1 is composed of 255 amino acids including a signal peptide at N-terminal followed by a putative activation peptide and the mature protein along with five putative phosphorylation sites, three disulphide bridges, and two N-glycosylation positions. At least nine conserved motifs were obtained in multiple sequence alignments. Some conserved residues, such as the catalytic triad His84, Asp127, and Ser229 as well as six cysteines at position 66, 82, 194, 211, 223, and 247, were examined. After homology modeling and molecular dynamics simulation, the resultant three-dimensional (3D) structure of SlSP1 was docked with the substrates 2PTC-Arg and 2PTC-Lys, respectively. Molecular Mechanic/Poisson-Boltzmann surface area analysis was applied to anticipate optimal binding mode and crucial active sites of this enzyme. The residues Trp28, Gly187, Aso188, Arg249, Ile250, Lys246, and Lys278 are crucial for the substrate binding and molecule process. This information can be used in logical design of SPs inhibitors. New inhibitors may be a basis for development of a new pest control technology.
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Affiliation(s)
- Li Yang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
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11
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Dong L, Shi J, Liu Y. Theoretical studies on the interaction of biphenyl inhibitors with Mycobacterium tuberculosis protein tyrosine phosphatase MptpB. J Mol Model 2012; 18:3847-56. [DOI: 10.1007/s00894-012-1384-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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12
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Labbé DP, Hardy S, Tremblay ML. Protein tyrosine phosphatases in cancer: friends and foes! PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 106:253-306. [PMID: 22340721 DOI: 10.1016/b978-0-12-396456-4.00009-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tyrosine phosphorylation of proteins serves as an exquisite switch in controlling several key oncogenic signaling pathways involved in cell proliferation, apoptosis, migration, and invasion. Since protein tyrosine phosphatases (PTPs) counteract protein kinases by removing phosphate moieties on target proteins, one may intuitively think that PTPs would act as tumor suppressors. Indeed, one of the most described PTPs, namely, the phosphatase and tensin homolog (PTEN), is a tumor suppressor. However, a growing body of evidence suggests that PTPs can also function as potent oncoproteins. In this chapter, we provide a broad historical overview of the PTPs, their mechanism of action, and posttranslational modifications. Then, we focus on the dual properties of classical PTPs (receptor and nonreceptor) and dual-specificity phosphatases in cancer and summarize the current knowledge of the signaling pathways regulated by key PTPs in human cancer. In conclusion, we present our perspective on the potential of these PTPs to serve as therapeutic targets in cancer.
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Affiliation(s)
- David P Labbé
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
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Molecular dynamics simulation of the interaction between protein tyrosine phosphatase 1B and aryl diketoacid derivatives. J Mol Graph Model 2012; 38:186-93. [PMID: 23085163 DOI: 10.1016/j.jmgm.2012.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/28/2012] [Accepted: 06/28/2012] [Indexed: 11/22/2022]
Abstract
The protein tyrosine phosphatase 1B (PTP-1B) is acknowledged as an outstanding therapeutic target for the treatment of diabetes, obesity and cancer. In this work, six aryl diketoacid compounds have been studied on the basis of molecular dynamics simulations. Hydrogen bonds, binding energies and conformation changes of the WPD loop have been analyzed. The results indicated that their activation model falls into two parts: the target region of the monomeric aryl diketoacid compounds is the active site, whereas the target region of the dimeric aryl diketoacid compounds is the WPD loop or the R loop. The van der Waals interactions exhibit stronger effects than the short-range electrostatic interactions. The van der Waals interaction energy and the IC50 values exhibit an approximately exponential relationship. Furthermore, the van der Waals interactions cooperate with the hydrogen bond interactions. This study provides a more thorough understanding of the PTP-1B inhibitor binding processes.
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Effect of a novel proteoglycan PTP1B inhibitor from Ganoderma lucidum on the amelioration of hyperglycaemia and dyslipidaemia in db/db mice. Br J Nutr 2012; 108:2014-25. [PMID: 22453054 DOI: 10.1017/s0007114512000153] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is implicated in the negative regulation of the insulin signalling pathway by dephosphorylating the insulin receptor (IR) and IR substrates. Ganoderma lucidum has traditionally been used for the treatment of diabetes in Chinese medicine; however, its anti-diabetic potency and mechanism in vivo is still unclear. Our previously published study reported a novel proteoglycan PTP1B inhibitor, named Fudan-Yueyang-Ganoderma lucidum (FYGL) from G. lucidum, with a half-maximal inhibitory concentration (IC₅₀) value of 5·12 (sem 0·05) μg/ml, a protein:polyglycan ratio of 17:77 and 78 % glucose in polysaccharide, and dominant amino acid residues of aspartic acid, glycine, glutamic acid, alanine, serine and threonine in protein. FYGL is capable of decreasing plasma glucose in streptozotocin-induced diabetic mice with a high safety of median lethal dose (LD₅₀) of 6 g/kg. In the present study, C57BL/6 db/db diabetic mice were trialed further using FYGL as well as metformin for comparison. Oral treatment with FYGL in db/db diabetic mice for 4 weeks significantly (P < 0·01 or 0·05) decreased the fasting plasma glucose level, serum insulin concentration and the homeostasis model assessment of insulin resistance. FYGL also controlled the biochemistry indices relative to type 2 diabetes-accompanied lipidaemic disorders. Pharmacology research suggests that FYGL decreases the plasma glucose level by the mechanism of inhibiting PTP1B expression and activity, consequently, regulating the tyrosine phosphorylation level of the IR β-subunit and the level of hepatic glycogen, thus resulting in the improvement of insulin sensitivity. Therefore, FYGL is promising as an insulin sensitiser for the therapy of type 2 diabetes and accompanied dyslipidaemia.
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15
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Structural flexibility and interactions of PTP1B’s S-loop. Interdiscip Sci 2009; 1:214-9. [DOI: 10.1007/s12539-009-0047-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 04/19/2009] [Accepted: 04/23/2009] [Indexed: 11/26/2022]
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Wang JF, Gong K, Wei DQ, Li YX, Chou KC. Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one. Protein Eng Des Sel 2009; 22:349-55. [PMID: 19380334 DOI: 10.1093/protein/gzp012] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein tyrosine phosphatases 1B (PTP1B) is a major negative regulator of both insulin and leptin signaling pathways. In view of this, it becomes an important target for drug development against cancers, diabetes and obesity. The aim of the current study is to use the long time-scale molecular dynamics (MD) simulations to investigate the structural and dynamic factors that cause its inhibition by INTA and INTB, the two most potent and highly selective PTP1B inhibitors known so far. In order to investigate the mode of collective motions that is vitally important to the biological function, the covariance matrix of C(alpha) atoms was introduced for performing the dynamic analysis of the inhibition systems. It has been observed that the conformational and dynamic features of WPD-Loop, R-Loop and S-Loop play a key role in providing a smooth entrance for the inhibitors moving into the binding pocket as well as a favorable microenvironment to stabilize them. Furthermore, the hydrogen bonding networks formed around the active site with INTA and INTB may be the main reason of why the inhibition of PTP1B by the two ligands is so potent and selective. All these findings might provide useful insights for developing novel and effective drugs to treat cancer, diabetes and obesity.
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Affiliation(s)
- Jing-Fang Wang
- Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Peoples Republic of China
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Pauli I, Caceres RA, de Azevedo WF. Molecular modeling and dynamics studies of Shikimate Kinase from Bacillus anthracis. Bioorg Med Chem 2008; 16:8098-108. [PMID: 18706819 DOI: 10.1016/j.bmc.2008.07.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 07/17/2008] [Accepted: 07/19/2008] [Indexed: 11/16/2022]
Abstract
Bacillus anthracis has been used as weapon in bioterrorist activities, with high mortality, despite anti-microbial treatment, which strongly indicates a need of new drugs to treat anthrax. Shikimate Pathway is a seven-step biosynthetic route which generates chorismic acid. The shikimate pathway is essential for many pathological organisms, whereas it is absent in mammals. Therefore, these enzymes are potential targets for the development of non-toxic anti-microbial agents and herbicides and have been submitted to intensive structural studies. Shikimate Kinase is the fifth enzyme of shikimate pathway and catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimate using ATP as a co-substrate, resulting in shikimate-3-phosphate and ADP. The present work describes for the first time a structural model for the Shikimate Kinase from B. anthracis using molecular modeling approach and molecular dynamics simulations. This study was able to identify the main residues of the ATP-binding and the shikimate pockets responsible for ligand affinities. Analysis of the molecular dynamics simulations indicates the structural features responsible for the stability of the structure. This study may help in the identification of new inhibitors for this enzyme.
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Affiliation(s)
- Ivani Pauli
- Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga, 6681, Porto Alegre, 90619-900 Rio Grande do Sul, CEP, Brazil
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