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Recent Updates on Development of Protein-Tyrosine Phosphatase 1B Inhibitors for Treatment of Diabetes, Obesity and Related Disorders. Bioorg Chem 2022; 121:105626. [DOI: 10.1016/j.bioorg.2022.105626] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/19/2021] [Accepted: 01/13/2022] [Indexed: 01/30/2023]
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Discovery of inhibitors targeting protein tyrosine phosphatase 1B using a combined virtual screening approach. Mol Divers 2021; 26:2159-2174. [PMID: 34655403 DOI: 10.1007/s11030-021-10323-2] [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: 06/14/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) acts as a therapeutic target for type 2 diabetes. However, the major challenges of PTP1B drug discovery are the poor selectivity and the weak oral bioavailability. In this study, we performed a combined virtual screening approach including multicomplex pharmacophore, molecular docking-based screening, van der Waals energy normalization, pose scaling factor, ADMET evaluation, and molecular dynamics simulation to select PTP1B inhibitors from three databases (PubChem, ChEMBL, and ZINC). We identified three potential PTP1B inhibitors, compounds 1, 4, and 5, with favorable binding energy and good oral bioavailability. The energetic and geometrical analyses show that the three compounds are stably bound to PTP1B, via occupying both the catalytic site (site A) and the proximal noncatalytic site (site B or C). Such occupancy may improve the selectivity. This work not only provided a feasible virtual screening protocol, but also suggested three potential PTP1B inhibitors for the treatment of type 2 diabetes.
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Yuan F, Xie S, Zhuo L, Wang L, Zhu H. Metal‐Free Synthesis of 2‐Aryl Quinazolines via Tandem C−H/N−H Bond Functionalization. ChemistrySelect 2021. [DOI: 10.1002/slct.202100990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Feixiang Yuan
- College of Chemistry and Molecular Engineering Nanjing Tech University No. 30 North Puzhu Road Nanjing 211816 P. R. China
| | - Shihua Xie
- College of Chemistry and Molecular Engineering Nanjing Tech University No. 30 North Puzhu Road Nanjing 211816 P. R. China
| | - Liang Zhuo
- College of Chemistry and Molecular Engineering Nanjing Tech University No. 30 North Puzhu Road Nanjing 211816 P. R. China
| | - Lei Wang
- College of Chemistry and Molecular Engineering Nanjing Tech University No. 30 North Puzhu Road Nanjing 211816 P. R. China
| | - Hongjun Zhu
- College of Chemistry and Molecular Engineering Nanjing Tech University No. 30 North Puzhu Road Nanjing 211816 P. R. China
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Kousaxidis A, Petrou A, Lavrentaki V, Fesatidou M, Nicolaou I, Geronikaki A. Aldose reductase and protein tyrosine phosphatase 1B inhibitors as a promising therapeutic approach for diabetes mellitus. Eur J Med Chem 2020; 207:112742. [PMID: 32871344 DOI: 10.1016/j.ejmech.2020.112742] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus is a metabolic disease characterized by high blood glucose levels and usually associated with several chronic pathologies. Aldose reductase and protein tyrosine phosphatase 1B enzymes have identified as two novel molecular targets associated with the onset and progression of type II diabetes and related comorbidities. Although many inhibitors against these enzymes have already found in the field of diabetic mellitus, the research for discovering more effective and selective agents with optimal pharmacokinetic properties continues. In addition, dual inhibition of these target proteins has proved as a promising therapeutic approach. A variety of diverse scaffolds are presented in this review for the future design of potent and selective inhibitors of aldose reductase and protein tyrosine phosphatase 1B based on the most important structural features of both enzymes. The discovery of novel dual aldose reductase and protein tyrosine phosphatase 1B inhibitors could be effective therapeutic molecules for the treatment of insulin-resistant type II diabetes mellitus. The methods used comprise a literature survey and X-ray crystal structures derived from Protein Databank (PDB). Despite the available therapeutic options for type II diabetes mellitus, the inhibitors of aldose reductase and protein tyrosine phosphatase 1B could be two promising approaches for the effective treatment of hyperglycemia and diabetes-associated pathologies. Due to the poor pharmacokinetic profile and low in vivo efficacy of existing inhibitors of both targets, the research turned to more selective and cell-permeable agents as well as multi-target molecules.
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Affiliation(s)
- Antonios Kousaxidis
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Anthi Petrou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Vasiliki Lavrentaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Maria Fesatidou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Ioannis Nicolaou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Athina Geronikaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece.
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Eleftheriou P, Geronikaki A, Petrou A. PTP1b Inhibition, A Promising Approach for the Treatment of Diabetes Type II. Curr Top Med Chem 2019; 19:246-263. [PMID: 30714526 DOI: 10.2174/1568026619666190201152153] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 01/07/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND Diabetes Mellitus (DM), is a metabolic disorder characterized by high blood glucose levels. The main types of diabetes mellitus are Diabetes mellitus type I, Diabetes mellitus type II, gestational diabetes and Diabetes of other etiology. Diabetes type II, the Non Insulin Dependent Type (NIDDM) is the most common type, characterized by the impairment in activation of the intracellular mechanism leading to the insertion and usage of glucose after interaction of insulin with its receptor, known as insulin resistance. Although, a number of drugs have been developed for the treatment of diabetes type II, their ability to reduce blood glucose levels is limited, while several side effects are also observed. Furthermore, none of the market drugs targets the enhancement of the action of the intracellular part of insulin receptor or recuperation of the glucose transport mechanism in GLUT4 dependent cells. The Protein Tyrosine Phosphatase (PTP1b) is the main enzyme involved in insulin receptor desensitization and has become a drug target for the treatment of Diabetes type II. Several PTP1b inhibitors have already been found, interacting with the binding site of the enzyme, surrounding the catalytic amino acid Cys215 and the neighboring area or with the allosteric site of the enzyme, placed at a distance of 20 Å from the active site, around Phe280. However, the research continues for finding more potent inhibitors with increased cell permeability and specificity. OBJECTIVE The aim of this review is to show the attempts made in developing of Protein Tyrosine Phosphatase (PTP1b) inhibitors with high potency, selectivity and bioavailability and to sum up the indications for favorable structural characteristics of effective PTP1b inhibitors. METHODS The methods used include a literature survey and the use of Protein Structure Databanks such as PuBMed Structure and RCSB and the tools they provide. CONCLUSION The research for finding PTP1b inhibitors started with the design of molecules mimicking the Tyrosine substrate of the enzyme. The study revealed that an aromatic ring connected to a polar group, which preferably enables hydrogen bond formation, is the minimum requirement for small inhibitors binding to the active site surrounding Cys215. Molecules bearing two hydrogen bond donor/acceptor (Hb d/a) groups at a distance of 8.5-11.5 Å may form more stable complexes, interacting simultaneously with a secondary area A2. Longer molecules with two Hb d/a groups at a distance of 17 Å or 19 Å may enable additional interactions with secondary sites (B and C) that confer stability as well as specificity. An aromatic ring linked to polar or Hb d/a moieties is also required for allosteric inhibitors. A lower distance between Hb d/a moieties, around 7.5 Å may favor allosteric interaction. Permanent inhibition of the enzyme by oxidation of the catalytic Cys215 has also been referred. Moreover, covalent modification of Cys121, placed near but not inside the catalytic pocket has been associated with permanent inhibition of the enzyme.
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Affiliation(s)
- Phaedra Eleftheriou
- Department of Medical Laboratory Studies, School of Health and Medical Care, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki 57400, Greece
| | - Athina Geronikaki
- Department of Pharmacy, School of Health, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Anthi Petrou
- Department of Pharmacy, School of Health, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
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The development of protein tyrosine phosphatase1B inhibitors defined by binding sites in crystalline complexes. Future Med Chem 2019; 10:2345-2367. [PMID: 30273014 DOI: 10.4155/fmc-2018-0089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Protein tyrosine phosphatase1B (PTP1B), a significant negative regulator in insulin and leptin signaling pathways, has emerged as a promising drug target for Type II diabetes mellitus and obesity. Numerous potent PTP1B inhibitors have been discovered within both academia and pharmaceutical industry. However, nearly all medicinal chemistry efforts have been severely hindered because a vast majority of them demonstrate poor membrane permeability and low-selectivity, especially over T-cell protein tyrosine phosphatase (TCPTP). To search the rules about the selectivity over TCPTP and membrane permeability of PTP1B inhibitors, based on the PTP1B/inhibitor crystal complexes, the development PTP1B inhibitors defined as AB, AC, ABC and ADC types have been concluded in the review.
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7
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Toward the identification of a reliable 3D-QSAR model for the protein tyrosine phosphatase 1B inhibitors. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kumar AP, Nguyen MN, Verma C, Lukman S. Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites. Proteins 2018; 86:301-321. [PMID: 29235148 DOI: 10.1002/prot.25440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/16/2017] [Accepted: 12/10/2017] [Indexed: 12/11/2022]
Abstract
Catalytic proteins such as human protein tyrosine phosphatase 1B (PTP1B), with conserved and highly polar active sites, warrant the discovery of druggable nonactive sites, such as allosteric sites, and potentially, therapeutic small molecules that can bind to these sites. Catalyzing the dephosphorylation of numerous substrates, PTP1B is physiologically important in intracellular signal transduction pathways in diverse cell types and tissues. Aberrant PTP1B is associated with obesity, diabetes, cancers, and neurodegenerative disorders. Utilizing clustering methods (based on root mean square deviation, principal component analysis, nonnegative matrix factorization, and independent component analysis), we have examined multiple PTP1B structures. Using the resulting representative structures in different conformational states, we determined consensus clustroids and used them to identify both known and novel binding sites, some of which are potentially allosteric. We report several lead compounds that could potentially bind to the novel PTP1B binding sites and can be further optimized. Considering the possibility for drug repurposing, we discovered homologous binding sites in other proteins, with ligands that could potentially bind to the novel PTP1B binding sites.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Minh N Nguyen
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:3636-3650. [DOI: 10.1080/07391102.2017.1394221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
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Liang L, Wang J, Shi X, Zhu Y, Li J, Zhu W, Wang H, Guo Y. A Novel Sarsolenane Diterpene as a PTP1B Inhibitor from Hainan Soft Coral Sarcophyton trocheliophorum
Marenzeller. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Linfu Liang
- College of Material Science and Engineering; Central South University of Forestry and Technology; Changsha Hunan 410004 China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
| | - Jinan Wang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
| | - Xiaoxuan Shi
- College of Material Science and Engineering; Central South University of Forestry and Technology; Changsha Hunan 410004 China
| | - Yinghua Zhu
- College of Material Science and Engineering; Central South University of Forestry and Technology; Changsha Hunan 410004 China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
| | - Heyao Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
| | - Yuewei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
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Lakshmi Narayana Sharma K, Suresh Kumar C, Kumaraswamy S, Krishna Reddy V, Kameswara Rao N, Raghu Babu K, Ramakrishna G. Palladium-catalyzed domino sequence for the synthesis of N-aryl quinolinone-3-carboxylate derivatives and their anti-proliferative activity. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Meng G, Zheng M, Wang M, Tong J, Ge W, Zhang J, Zheng A, Li J, Gao L, Li J. Design and synthesis of new potent PTP1B inhibitors with the skeleton of 2-substituted imino-3-substituted-5-heteroarylidene-1,3-thiazolidine-4-one: Part I. Eur J Med Chem 2016; 122:756-769. [PMID: 27526040 DOI: 10.1016/j.ejmech.2016.05.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/26/2016] [Accepted: 05/26/2016] [Indexed: 11/19/2022]
Abstract
A new series of 2-substituted imino-3-substituted-5- heteroarylidene-1,3-thiazolidine-4-ones as the potent bidentate PTP1B inhibitors were designed and synthesized in this paper. All of the new compounds were characterized and identified by spectra analysis. The biological screening test against PTP1B showed that some of these compounds have the positive inhibitory activity against PTP1B. The activity of the compounds with 5-substituted pyrrole on 5-postion of 1,3-thiazolidine-4-one are more potent than that of those compounds with 5-substituted pyridine group. Compound 14b, 14h and 14i showed IC50 values of 8.66 μM, 6.83 μM and 6.09 μM against PTP1B, respectively. Docking analysis of these active compounds with PTP1B showed the possible interaction modes of these biheterocyclic compounds with the active sites of PTP1B. The inhibition tests against oncogenetic CDC25B were also conducted on this set of compounds to evaluate the selectivity and possible anti-neoplastic activity. Compound 14b also showed the lowest IC50 of 1.66 μM against CDC25B among all the possible inhibitors, including 14g, 14h, 14i and 15c. Some pharmacological parameters including VolSurf, steric and electric descriptors of all the compounds were calculated to give some hints about the relative relationship with the biological activity. The result of this study might give some light on designing the possible anti-cancer drugs targeting at phosphatases. The most active compound 14i might be used as the lead compound for further structure modification of the new low molecular weight PTP1B inhibitors with the N-containing heterocyclic skeleton.
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Affiliation(s)
- Ge Meng
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China.
| | - Meilin Zheng
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Mei Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Jing Tong
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Weijuan Ge
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Jiehe Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Aqun Zheng
- School of Science, Xi'an Jiaotong University, No. 28, Xianning West Road, Xi'an, Shaanxi, 710049, PR China
| | - Jingya Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Lixin Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
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The design strategy of selective PTP1B inhibitors over TCPTP. Bioorg Med Chem 2016; 24:3343-52. [PMID: 27353889 DOI: 10.1016/j.bmc.2016.06.035] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 02/01/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has already been well studied as a highly validated therapeutic target for diabetes and obesity. However, the lack of selectivity limited further studies and clinical applications of PTP1B inhibitors, especially over T-cell protein tyrosine phosphatase (TCPTP). In this review, we enumerate the published specific inhibitors of PTP1B, discuss the structure-activity relationships by analysis of their X-ray structures or docking results, and summarize the characteristic of selectivity related residues and groups. Furthermore, the design strategy of selective PTP1B inhibitors over TCPTP is also proposed. We hope our work could provide an effective way to gain specific PTP1B inhibitors.
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Li Y, Hari DP, Vita MV, Waser J. Cyclic Hypervalent Iodine Reagents for Atom-Transfer Reactions: Beyond Trifluoromethylation. Angew Chem Int Ed Engl 2016; 55:4436-54. [DOI: 10.1002/anie.201509073] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Yifan Li
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Switzerland
| | - Durga Prasad Hari
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Switzerland
| | - Maria Victoria Vita
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Switzerland
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15
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Li Y, Hari DP, Vita MV, Waser J. Cyclische hypervalente Iodreagentien für Atomtransferreaktionen - jenseits der Trifluormethylierung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509073] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yifan Li
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Schweiz
| | - Durga Prasad Hari
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Schweiz
| | - Maria Victoria Vita
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Schweiz
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis; Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO; BCH 4306 1015 Lausanne CH Schweiz
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16
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Eleftheriou P, Petrou A, Geronikaki A, Liaras K, Dirnali S, Anna M. Prediction of enzyme inhibition and mode of inhibitory action based on calculation of distances between hydrogen bond donor/acceptor groups of the molecule and docking analysis: An application on the discovery of novel effective PTP1B inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:557-576. [PMID: 26294069 DOI: 10.1080/1062936x.2015.1074939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 07/16/2015] [Indexed: 06/04/2023]
Abstract
PTP1B is a protein tyrosine phosphatase involved in insulin receptor desensitization. PTP1B inhibition prolongs the activated state of the receptor, practically enhancing the effect of insulin. Thus PTP1B has become a drug target for the treatment of type II diabetes. PTP1b is an enzyme with multiple binding sites for competitive and allosteric inhibitors. Prediction of inhibitory action using docking analysis has limited success in case of enzymes with multiple binding sites, since the selection of the right crystal structure depends on the kind of inhibitor. In the present study, a two-step strategy for the prediction of PTP1b inhibitory action was applied to 12 compounds. Based on the study of known inhibitors, we isolated the structural characteristics required for binding to each binding site. As a first step, 3D-structures of the molecules were produced and their structural parameters were measured and used for prediction of the binding site of the compound. These results were used for the selection of the appropriate crystal structure for docking analysis of each compound, and the final prediction was based on the estimated binding energies. This strategy effectively predicted the activity of all compounds. A linear correlation was found between estimated binding energy and inhibition measured in vitro (r = -0.894).
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Affiliation(s)
- P Eleftheriou
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Greece
| | - A Petrou
- b Department of Medicinal Chemistry, School of Medicine , Aristotle University of Thessaloniki , Greece
| | - A Geronikaki
- b Department of Medicinal Chemistry, School of Medicine , Aristotle University of Thessaloniki , Greece
| | - K Liaras
- b Department of Medicinal Chemistry, School of Medicine , Aristotle University of Thessaloniki , Greece
| | - S Dirnali
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Greece
| | - M Anna
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Greece
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Abstract
SIGNIFICANCE Protein tyrosine phosphatases (PTPs) are important enzymes that are involved in the regulation of cellular signaling. Evidence accumulated over the years has indicated that PTPs present exciting opportunities for drug discovery against diseases such as diabetes, cancer, autoimmune diseases, and tuberculosis. However, the highly conserved and partially positive charge of the catalytic sites of PTPs is a major challenge in the development of potent and highly selective PTP inhibitors. RECENT ADVANCES Here, we examine the strategy of developing bidentate inhibitors for selective inhibition of PTPs. Bidentate inhibitors are small-molecular-weight compounds with the ability to bind to both the active site and a non-conserved secondary phosphate binding site. This secondary phosphate binding site was initially discovered in protein tyrosine phosphatase 1B (PTP1B), and, hence, most of the bidentate inhibitors reported in this review are PTP1B inhibitors. CRITICAL ISSUES Although bidentate inhibition is a good strategy for developing potent and selective inhibitors, the cell membrane permeability and pharmacokinetic properties of the inhibitors are also important for successful drug development. In this review, we will also summarize the various efforts made toward the development of phosphotyrosine (pTyr) mimetics for increasing cellular permeability. FUTURE DIRECTIONS Even though the secondary phosphate binding site was initially found in PTP1B, structural data have shown that a secondary binding site can also be found in other PTPs, albeit with varying degrees of accessibility. Along with improvements in pTyr mimetics, we believe that the future will see an increase in the number of orally bioavailable bidentate inhibitors against the various classes of PTPs.
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Affiliation(s)
- Joo-Leng Low
- 1 Institute of Chemical and Engineering Sciences , Agency for Science Technology and Research, Singapore, Singapore
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18
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Yusubov MS, Yusubova RY, Nemykin VN, Zhdankin VV. Preparation and X-ray Structural Study of 1-Arylbenziodoxolones. J Org Chem 2013; 78:3767-73. [DOI: 10.1021/jo400212u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mekhman S. Yusubov
- The Siberian State Medical University and The Tomsk Polytechnic University, 634050 Tomsk, Russia
| | - Roza Y. Yusubova
- The Siberian State Medical University and The Tomsk Polytechnic University, 634050 Tomsk, Russia
| | - Victor N. Nemykin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota,
55812, United States
| | - Viktor V. Zhdankin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota,
55812, United States
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Abstract
The SHAPES method is one of several fragment-based drug discovery methods developed in the last decade. Molecules containing drug-like fragments are screened using NMR methods to find weakly binding (0.1 μM to multi-mM) hits that are then transformed into potent, viable leads. This review analyzes ten years of SHAPES screens, in which potent leads were found for 70 - 80% of the targets screened, and discusses lessons learned about how best to apply fragment-based lead discovery in the pharmaceutical environment. Detailed examples of lead discovery and optimization for the kinases REDK and MK2 are given. Finally, future directions are considered and a strategy is proposed for increasing efficiency by coupling fragment-based screening with receptor-assisted inhibitor design (NMR-RAID).
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Affiliation(s)
- Christopher Lepre
- Vertex Pharmaceuticals, Inc., 130 Waverly Street, Cambridge, MA 02139, USA +1 617 444 6627 ;
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Maccari R, Ottanà R. Low molecular weight phosphotyrosine protein phosphatases as emerging targets for the design of novel therapeutic agents. J Med Chem 2011; 55:2-22. [PMID: 21988196 DOI: 10.1021/jm200607g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rosanna Maccari
- Dipartimento Farmaco-Chimico, Faculty of Pharmacy, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy.
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Köster H, Craan T, Brass S, Herhaus C, Zentgraf M, Neumann L, Heine A, Klebe G. A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes. J Med Chem 2011; 54:7784-96. [PMID: 21972967 DOI: 10.1021/jm200642w] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.
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Affiliation(s)
- Helene Köster
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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22
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Ma L, Lu L, Zhu M, Wang Q, Gao F, Yuan C, Wu Y, Xing S, Fu X, Mei Y, Gao X. Dinuclear copper complexes of organic claw: potent inhibition of protein tyrosine phosphatases. J Inorg Biochem 2011; 105:1138-47. [PMID: 21708098 DOI: 10.1016/j.jinorgbio.2011.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 05/20/2011] [Accepted: 05/20/2011] [Indexed: 12/31/2022]
Abstract
Three dinuclear copper complexes of organic claw ligands (2,2',2″,2'''-(5-R-2-hydroxy-1,3-phenylene)bis(methylene)bis(azanetriyl)tetraacetic acid, R=methyl (H(5)L1), chloro (H(5)L2) and bromo (H(5)L3)): [Cu(2)NaL1(H(2)O)(2)] (1), [Cu(2)HL2(H(2)O)(2)] (2), [Cu(2)NaL3(H(2)O)(2)] (3), have been synthesized and characterized by elemental analyses, infrared spectra, thermo-gravimetric analyses, X-ray diffraction analysis, electrospray ionization mass spectra, pH-potentiometric titration, molar conductivity. Their inhibitory effects against human protein tyrosine phosphatase 1B (PTP1B), T cell protein tyrosine phosphatase (TCPTP), Megakaryocyte protein tyrosinephosphatase 2 (PTP-MEG2), srchomology phosphatase 1 (SHP-1) and srchomology phosphatase 2 (SHP-2) are evaluated in vitro. The three copper complexes exhibit potent and almost same inhibition against PTP1B and SHP-1 with IC(50) values ranging from 0.15 to 0.31μM, about 2-fold stronger inhibition than against PTP-MEG2, 10-fold stronger inhibition than against TCPTP, but almost no inhibition against SHP-2. Kinetic analysis indicates that they are reversible competitive inhibitors of PTP1B. Molecular docking analyses confirm the inhibition model. Fluorescence titration studies suggest that the complexes bond to PTP1B with the formation of a 1:1 complex. The results demonstrate that copper complexes that are potent PTPs inhibitors but have different inhibitory effects over different PTPs, may be explored as new practical inhibitors towards individual PTP with some specificity.
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Affiliation(s)
- Ling Ma
- Institute of Molecular Science, the Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Shanxi University, Taiyuan, 030006, China
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Thareja S, Aggarwal S, Bhardwaj TR, Kumar M. Protein Tyrosine Phosphatase 1B Inhibitors: A Molecular Level Legitimate Approach for the Management of Diabetes Mellitus. Med Res Rev 2010; 32:459-517. [DOI: 10.1002/med.20219] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Suresh Thareja
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
| | - Saurabh Aggarwal
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
| | | | - Manoj Kumar
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
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Abstract
The shape of the protein surface dictates what interactions are possible with other macromolecules, but defining discrete pockets or possible interaction sites remains difficult. First, there is the problem of defining the extent of the pocket. Second, one has to characterize the shape of each pocket. Third, one needs to make quantitative comparisons between pockets on different proteins. An elegant solution to these problems is to sort all surface and solvent points by travel depth and then collect a hierarchical tree of pockets. The connectivity of the tree is determined via the deepest saddle points between each pair of neighboring pockets. The resulting pocket surfaces tessellate the entire protein surface, producing a complete inventory of pockets. This method of identifying pockets also allows one to easily compute important shape metrics, including the problematic pocket volume, surface area, and mouth size. Pockets are also annotated with their lining residue lists and polarity and with other residue-based properties. Using this tree and the various shape metrics pockets can be merged, grouped, or filtered for further analysis. Since this method includes the entire surface, it guarantees that any pocket of interest will be found among the output pockets, unlike all previous methods of pocket identification. The resulting hierarchy of pockets is easy to visualize and aids users in higher level analysis. Comparison of pockets is done by using the shape metrics, avoiding the complex shape alignment problem. Example applications show that the method facilitates pocket comparison along mutational or time-dependent series. Pockets from families of proteins can be examined using multiple pocket tree alignments to see how ligand binding sites or how other pockets have changed with evolution. Our method is called CLIPPERS for complete liberal inventory of protein pockets elucidating and reporting on shape.
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Affiliation(s)
- Ryan G Coleman
- Department of Biochemistry and Biophysics, The Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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New strategies in fighting TB: targeting Mycobacterium tuberculosis-secreted phosphatases MptpA & MptpB. Future Med Chem 2010; 2:1325-37. [DOI: 10.4155/fmc.10.214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Mycobacterium tuberculosis is the most successful human pathogen due to its ability to challenge the innate immune system and survive in the infected host for a lifetime. Although tuberculosis (TB) is a curable disease, severe multidrug resistance to traditional antibiotics has caused a resurgence of the infection worldwide. The secreted phosphatases MptpA and MptpB are key virulence factors that play important roles in survival of M. tuberculosis during macrophage infection. These enzymes are therefore attractive alternative targets for chemotherapy. In this review we analyze the structural features that characterize these two phosphatases and differentiate them from human homologs. Their structural peculiarities are important for drug-design considerations and the future development of selective inhibitors. We describe the recent efforts in developing specific, selective and cell-active inhibitors of MptpA and MptpB, and discuss their potential applications as alternative treatments of TB.
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Singh R, Sobhia ME. Synergistic application of target structure-based alignment and 3D-QSAR study of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9365-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Zhang X, Li X, Wang R. Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function. J Chem Inf Model 2009; 49:1033-48. [DOI: 10.1021/ci8004429] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xinglong Zhang
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Xun Li
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
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Ottanà R, Maccari R, Ciurleo R, Paoli P, Jacomelli M, Manao G, Camici G, Laggner C, Langer T. 5-Arylidene-2-phenylimino-4-thiazolidinones as PTP1B and LMW-PTP inhibitors. Bioorg Med Chem 2009; 17:1928-37. [DOI: 10.1016/j.bmc.2009.01.044] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/14/2009] [Accepted: 01/20/2009] [Indexed: 01/28/2023]
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29
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Beresford NJ, Mulhearn D, Szczepankiewicz B, Liu G, Johnson ME, Fordham-Skelton A, Abad-Zapatero C, Cavet JS, Tabernero L. Inhibition of MptpB phosphatase from Mycobacterium tuberculosis impairs mycobacterial survival in macrophages. J Antimicrob Chemother 2009; 63:928-36. [DOI: 10.1093/jac/dkp031] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mohler ML, He Y, Wu Z, Hwang DJ, Miller DD. Recent and emerging anti-diabetes targets. Med Res Rev 2009; 29:125-95. [DOI: 10.1002/med.20142] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Albarracin CA, Fuqua BC, Evans JL, Goldfine ID. Chromium picolinate and biotin combination improves glucose metabolism in treated, uncontrolled overweight to obese patients with type 2 diabetes. Diabetes Metab Res Rev 2008; 24:41-51. [PMID: 17506119 DOI: 10.1002/dmrr.755] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Chromium and biotin play essential roles in regulating carbohydrate metabolism. This randomized, double-blind, placebo-controlled study evaluated the efficacy and safety of the combination of chromium picolinate and biotin on glycaemic control. METHODS Four hundred and forty-seven subjects with poorly controlled type 2 diabetes (HbA(1c) > or = 7.0%) were enrolled and received either chromium picolinate (600 microg Cr(+3)) with biotin (2 mg), or matching placebo, for 90 days in combination with stable oral anti-diabetic agents (OADs). Major endpoints were reductions in HbA(1c), fasting glucose, and lipids. Safety and tolerability were assessed. RESULTS Change in HbA(1c) was significantly different between treatment groups (p = 0.03). HbA(1c) in the chromium picolinate/biotin group decreased 0.54%. The decrease in HbA(1c) was most pronounced in chromium picolinate/biotin subjects whose baseline HbA(1c) > or = 10%, and highly significant when compared with placebo (-1.76% vs - 0.68%; p = 0.005). Fasting glucose levels were reduced in the entire chromium picolinate/biotin group versus placebo (-9.8 mg/dL vs 0.7 mg/dL; p = 0.02). Reductions in fasting glucose were also most marked in those subjects whose baseline HbA(1c) > or = 10.0%, and significant when compared to placebo (-35.8 mg/dL vs. 16.2 mg/dL; p = 0.01). Treatment was well tolerated with no adverse effects dissimilar from placebo. CONCLUSIONS These results suggest that the chromium picolinate/biotin combination, administered as an adjuvant to current prescription anti-diabetic medication, can improve glycaemic control in overweight to obese individuals with type 2 diabetes; especially those patients with poor glycaemic control on oral therapy.
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Affiliation(s)
- Cesar A Albarracin
- Alpha Therapy Center, 4626 Weber Road, Suite 100, Corpus Christi, TX 78411, USA
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32
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Lee S, Wang Q. Recent development of small molecular specific inhibitor of protein tyrosine phosphatase 1B. Med Res Rev 2007; 27:553-73. [PMID: 17039461 DOI: 10.1002/med.20079] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein tyrosine phosphatases (PTPs), a large family of signaling enzymes, play essential roles in intracellular signal transduction by regulating the cellular level of tyrosine phosphorylation to control cell growth and differentiation, metabolism, cell migration, gene transcription, ion-channel activity, immune response, cell apoptosis, and bone development. Among all PTPs, protein tyrosine phosphatase 1B (PTP1B) plays a seminal role in cellular signaling and in many human diseases, including cancer, diabetes, and obesity. Therefore, small molecular inhibitors of PTP1B can be promising drug candidates. Because of the structural homologies in many families of PTPs, it is a challenging task to find inhibitors specific to each PTP. Recent studies suggested that secondary binding pockets or peripheral binding sites around the conserved active site should be exploited to design novel potent and selective PTP1B inhibitors. In this review, we discuss the structural and biological features of small molecular PTP1B-specific inhibitors, with particular emphasis on small molecular inhibitors targeting PTP1B over the other PTPs that have been synthesized in the past 4 years.
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Affiliation(s)
- Seokjoon Lee
- Department of Basic Science, Kwandong University College of Medicine, Gangneung 210-701, South Korea
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Maccari R, Paoli P, Ottanà R, Jacomelli M, Ciurleo R, Manao G, Steindl T, Langer T, Vigorita MG, Camici G. 5-Arylidene-2,4-thiazolidinediones as inhibitors of protein tyrosine phosphatases. Bioorg Med Chem 2007; 15:5137-49. [PMID: 17543532 DOI: 10.1016/j.bmc.2007.05.027] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 05/04/2007] [Accepted: 05/11/2007] [Indexed: 11/20/2022]
Abstract
4-(5-Arylidene-2,4-dioxothiazolidin-3-yl)methylbenzoic acids (2) were synthesized and evaluated in vitro as inhibitors of PTP1B and LMW-PTP, two protein tyrosine phosphatases (PTPs) which act as negative regulators of the metabolic and mitotic signalling of insulin. The synthesis of compounds 2 represents an example of utilizing phosphotyrosine-mimetics to identify effective low molecular weight nonphosphorus inhibitors of PTPs. Several thiazolidinediones 2 exhibited PTP1B inhibitory activity in the low micromolar range with moderate selectivity for human PTP1B and IF1 isoform of human LMW-PTP compared with other related PTPs.
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Affiliation(s)
- Rosanna Maccari
- Dipartimento Farmaco-Chimico, Università di Messina, Vl SS Annunziata, Messina, Italy.
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Zhao H. Scaffold selection and scaffold hopping in lead generation: a medicinal chemistry perspective. Drug Discov Today 2006; 12:149-55. [PMID: 17275735 DOI: 10.1016/j.drudis.2006.12.003] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/23/2006] [Accepted: 12/05/2006] [Indexed: 11/17/2022]
Abstract
Hit selection and lead generation are crucial for the success of the resource-demanding lead-optimization phase in drug discovery, and represent a major research area of medicinal chemistry today. Ligand-binding efficiency, ligand complexity, ligand-target profile complementarity and chemical tractability are important parameters in hit selection. As synthesis and assay throughput improve, a large number of analogs based on the same scaffold can be rapidly synthesized and tested. Consequently, more chemistry resources could be devoted to scaffold modifications to expand the candidate pool in lead generation. Most recently discovered druggable targets are promiscuous toward lipophilic ligands, and the hydrophobic portions of hit compounds should be preferentially modified in analog and scaffold design.
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Affiliation(s)
- Hongyu Zhao
- R4MC, AP-10, Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6098, USA.
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Abstract
The prevalence of obesity is increasing rapidly in most parts of the world and effective therapeutic drugs are urgently needed. The discovery of leptin in 1994 initiated a new understanding of adipose tissue function, and adipose tissue is now known to not only store and release fatty acids, but also to produce a wealth of factors that have an impact on the regulation of body weight and blood glucose homeostasis. Also, adipocytes express proteins that engage signalling pathways playing important roles in fuel substrate and energy metabolism. These proteins constitute a diverse array of adipose target candidates for the development of drugs to treat obesity. Some of these potential targets have been validated and are now in drug development stages, providing hope that the current obesity epidemic can be addressed by effective drug treatments in the near future.
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Asante-Appiah E, Patel S, Desponts C, Taylor JM, Lau C, Dufresne C, Therien M, Friesen R, Becker JW, Leblanc Y, Kennedy BP, Scapin G. Conformation-assisted Inhibition of Protein-tyrosine Phosphatase-1B Elicits Inhibitor Selectivity over T-cell Protein-tyrosine Phosphatase. J Biol Chem 2006; 281:8010-5. [PMID: 16407290 DOI: 10.1074/jbc.m511827200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PTP-1B represents an attractive target for the treatment of type 2 diabetes and obesity. Given the role that protein phosphatases play in the regulation of many biologically relevant processes, inhibitors against PTP-1B must be not only potent, but also selective. It has been extremely difficult to synthesize inhibitors that are selective over the highly homologous TCPTP. We have successfully exploited the conservative Leu119 to Val substitution between the two enzymes to synthesize a PTP-1B inhibitor that is an order of magnitude more selective over TCPTP. Structural analyses of PTP-1B/inhibitor complexes show a conformation-assisted inhibition mechanism as the basis for selectivity. Such an inhibitory mechanism may be applicable to other homologous enzymes.
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Affiliation(s)
- Ernest Asante-Appiah
- Department of Biochemistry and Molecular Biology, Merck Frosst Center for Therapeutic Research, Pointe-Claire, Dorval, Quebec H9R 4P8, Canada.
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38
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Rao GS, Ramachandran MV, Bajaj JS. In SilicoStructure-Based Design of a Potent and Selective Small Peptide Inhibitor of Protein Tyrosine Phosphatase 1B, A Novel Therapeutic Target for Obesity and Type 2 Diabetes Mellitus: A Computer Modeling Approach. J Biomol Struct Dyn 2006; 23:377-84. [PMID: 16363874 DOI: 10.1080/07391102.2006.10531233] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) has been shown to be a negative regulator of insulin signaling by dephosphorylating key tyrosine residues within the regulatory domain of the beta-subunit of the insulin receptor. Recent gene knockout studies in mice have shown the mice to have increased insulin sensitivity and improved glucose tolerance. Furthermore, these mice also exhibited a resistance to diet induced obesity. Inhibitors of PTP1B would have the potential of enhancing insulin action by prolonging the phosphorylated state of the insulin receptor. In addition, recent clinical studies have shown that the haplotype ACTTCAG0 of the PTPN1 gene, which encodes PTP1B, is a major risk contributor to type 2 diabetes mellitus (T2DM). Thus, there is compelling evidence that small molecule inhibitors of PTP1B may be effective in treating insulin resistance at an early stage, thereby leading to a prevention strategy for T2DM and obesity. Based on the crystal structure of the complex of PTP1B with a known inhibitor, we have identified a tetrapeptide inhibitor with the sequence WKPD. Docking calculations indicate that this peptide is as potent as the existing inhibitors. Moreover, the peptide is also found to be selective for PTP1B with a greatly reduced potency against other biologically important protein tyrosine phosphatases such as PTP-LAR, Calcineurin, and the highly homologous T-Cell Protein Tyrosine Phosphatase (TCPTP). Thus the designed tetrapeptide is a suitable lead compound for the development of new drugs against type 2 diabetes and obesity.
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Affiliation(s)
- Gita Subba Rao
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi - 110029, India.
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39
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Nichols AJ, Mashal RD, Balkan B. Toward the discovery of small molecule PTP1B inhibitors for the treatment of metabolic diseases. Drug Dev Res 2006. [DOI: 10.1002/ddr.20122] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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40
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Makara GM, Athanasopoulos J. Improving success rates for lead generation using affinity binding technologies. Curr Opin Biotechnol 2005; 16:666-73. [PMID: 16257522 PMCID: PMC7126921 DOI: 10.1016/j.copbio.2005.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 09/19/2005] [Accepted: 10/18/2005] [Indexed: 11/29/2022]
Abstract
Affinity technologies have been applied at several stages of the drug discovery process, ranging from target identification and purification to the identification of preclinical candidates. The detection of ligand–macromolecule interactions in lead discovery is the best studied and most powerful of these techniques. Although affinity methods have been in widespread use for about a decade, only recently have many reports emerged on their utility. Primary affinity screens of large libraries of small molecules or fragments have begun to produce results for challenging targets. Furthermore, in secondary assays affinity methods are opening new avenues to tackle important medicinal chemistry tasks.
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Affiliation(s)
- Gergely M Makara
- Merck Research Laboratories, Merck & Co., RY80Y-325, Rahway, New Jersey 07065, USA.
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41
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Holmes CP, Li X, Pan Y, Xu C, Bhandari A, Moody CM, Miguel JA, Ferla SW, De Francisco MN, Frederick BT, Zhou S, Macher N, Jang L, Irvine JD, Grove JR. Discovery and structure–activity relationships of novel sulfonamides as potent PTP1B inhibitors. Bioorg Med Chem Lett 2005; 15:4336-41. [PMID: 16046123 DOI: 10.1016/j.bmcl.2005.06.061] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 06/11/2005] [Accepted: 06/13/2005] [Indexed: 11/22/2022]
Abstract
A series of novel sulfonamides containing a single difluoromethylene-phosphonate group were discovered to be potent inhibitors of protein tyrosine phosphatase 1B. Structure-activity relationships around the scaffold were investigated, leading to the identification of compounds with IC50 or Ki values in the low nanomolar range. These sulfonamide-based inhibitors exhibit 100 and 30 times higher inhibitory activity than the corresponding tertiary amines and carboxamides, respectively.
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Pellecchia M, Becattini B, Crowell KJ, Fattorusso R, Forino M, Fragai M, Jung D, Mustelin T, Tautz L. NMR-based techniques in the hit identification and optimisation processes. Expert Opin Ther Targets 2005; 8:597-611. [PMID: 15584865 DOI: 10.1517/14728222.8.6.597] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this review, the use of general NMR spectroscopy techniques to detect ligand binding and to monitor enzyme kinetics and inhibition, which appear particularly useful in hit identification and validation, is reiterated. Furthermore, the use of NMR-based strategies for lead optimisations that are based on either iterative derivatisations of an initial core structure or on linking fragments that occupy adjacent pockets in the target's binding site will also be described. Several recent examples will be reported and the use of these techniques in cases when the three dimensional structure of the target protein is known will be discussed.
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Affiliation(s)
- Maurizio Pellecchia
- The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92103, USA.
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Abstract
Type 2 diabetes and obesity are characterised by insulin and leptin resistance. Studies suggest that these may be due to defects in the insulin and leptin signalling pathways. Over the last decade, a considerable body of evidence has been amassed indicating that protein tyrosine phosphatase 1B (PTP1B) is involved in the downregulation of insulin and leptin signalling. Consequently, compounds that inhibit PTP1B have potential as therapeutics for treating Type 2 diabetes and obesity. This review covers recent advances in PTP1B inhibitors with an emphasis on recent attempts to create potent, selective and cell-permeable small-molecule inhibitors.
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Affiliation(s)
- Scott D Taylor
- Department of Chemistry, University of Waterloo, Ontario, Canada.
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44
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Lepre CA, Moore JM, Peng JW. Theory and applications of NMR-based screening in pharmaceutical research. Chem Rev 2004; 104:3641-76. [PMID: 15303832 DOI: 10.1021/cr030409h] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher A Lepre
- Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139-4242, USA
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45
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Abstract
The genomics revolution has provided a deluge of new targets for drug discovery. To facilitate the drug discovery process, many researchers are turning to fragment-based approaches to find lead molecules more efficiently. One such method, Tethering1, allows for the identification of small-molecule fragments that bind to specific regions of a protein target. These fragments can then be elaborated, combined with other molecules, or combined with one another to provide high-affinity drug leads. In this review we describe the background and theory behind Tethering and discuss its use in identifying novel inhibitors for protein targets including interleukin-2 (IL-2), thymidylate synthase (TS), protein tyrosine phosphatase 1B (PTP-1B), and caspases.
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Affiliation(s)
- Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.
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46
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Liu G, Xin Z, Liang H, Abad-Zapatero C, Hajduk PJ, Janowick DA, Szczepankiewicz BG, Pei Z, Hutchins CW, Ballaron SJ, Stashko MA, Lubben TH, Berg CE, Rondinone CM, Trevillyan JM, Jirousek MR. Selective protein tyrosine phosphatase 1B inhibitors: targeting the second phosphotyrosine binding site with non-carboxylic acid-containing ligands. J Med Chem 2003; 46:3437-40. [PMID: 12877578 DOI: 10.1021/jm034088d] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein tyrosine phosphatase (PTPase) 1B (PTP1B) has been implicated as a key negative regulator of both insulin and leptin signaling cascades. We identified several salicylic acid-based ligands for the second phosphotyrosine binding site of PTP1B using a NMR-based screening. Structure-based linking with a catalytic site-directed oxalylarylaminobenzoic acid-based pharmacophore led to the identification of a novel series of potent PTP1B inhibitors exhibiting 6-fold selectivity over the highly homologous T-cell PTPase (TCPTP) and high selectivity over other phosphatases.
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Affiliation(s)
- Gang Liu
- Metabolic Disease Research and Advanced Technology, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064-6098, USA.
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