1
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Abu-Hashem AA, Abdelgawad AA, Gouda MA. Chemistry and Biological Activity of Thieno[3,4- b]quinoline, Thieno[3,4- c]
quinolone, Thieno[3,2- g]quinoline and Thieno[2,3- g]quinoline Derivatives:
A Review (Part IX). MINI-REV ORG CHEM 2024; 21:764-778. [DOI: 10.2174/1570193x20666230601151439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 07/10/2024]
Abstract
Abstract:
Over the previous decades, thieno-quinoline derivatives have acquired great interest due to
their synthetic and biological applications. These reports have been disclosed on Thienoquinoline
synthesis such as thieno[3,4-b]quinoline; thieno[3,4-c]quinolone; thieno [3,2-g]quinoline; thieno[2,3-
g] quinoline; spiro-thieno[2,3-g]quinoline; benzo[b]thiophen-iso- quinoline derivatives, and therefore
in the existent review, we provided an inclusive update on the synthesis of thienoquinolines. Characterization
of the preparation methods and reactivity is categorized based on their types of reactions as
addition, alkylation, chlorination, acylation, oxidation, reduction, cyclization and cyclo-condensation.
Hence, this study will help the researchers to obtain knowledge from the last literature research to
conquer their resolve problems in designing new compounds and processes.
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Affiliation(s)
- Ameen A. Abu-Hashem
- Chemistry Department, Faculty of Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Ahmed A.M. Abdelgawad
- Chemistry Department, Faculty of Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Moustafa A. Gouda
- Department of Chemistry,
Faculty of Science and Arts, Taibah University, Ulla, Medina, Saudi Arabia
- Department of Chemistry, Faculty of Science,
Mansoura University, Mansoura, 35516, Egypt
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2
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Zhang J, Li H, Zhao X, Wu Q, Huang SY. Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J Chem Inf Model 2022; 62:5806-5820. [PMID: 36342197 DOI: 10.1021/acs.jcim.2c00895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An important part in structure-based drug design is the selection of an appropriate protein structure. It has been revealed that a holo protein structure that contains a well-defined binding site is a much better choice than an apo structure in structure-based drug discovery. Therefore, it is valuable to obtain a holo-like protein conformation from apo structures in the case where no holo structure is available. Meeting the need, we present a robust approach to generate reliable holo-like structures from apo structures by ligand binding site refinement with restraints derived from holo templates with low homology. Our method was tested on a test set of 32 proteins from the DUD-E data set and compared with other approaches. It was shown that our method successfully refined the apo structures toward the corresponding holo conformations for 23 of 32 proteins, reducing the average all-heavy-atom RMSD of binding site residues by 0.48 Å. In addition, when evaluated against all the holo structures in the protein data bank, our method can improve the binding site RMSD for 14 of 19 cases that experience significant conformational changes. Furthermore, our refined structures also demonstrate their advantages over the apo structures in ligand binding mode predictions by both rigid docking and flexible docking and in virtual screening on the database of active and decoy ligands from the DUD-E. These results indicate that our method is effective in recovering holo-like conformations and will be valuable in structure-based drug discovery.
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Affiliation(s)
- Jinze Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Hao Li
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Xuejun Zhao
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Qilong Wu
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
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3
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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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4
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Niu C, Du DM. A squaramide-catalysed asymmetric cascade Michael addition/acyl transfer reaction between unsaturated benzothiophenones and α-nitroketones. Org Biomol Chem 2022; 20:840-846. [PMID: 35018912 DOI: 10.1039/d1ob02217b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An efficient and practical organocatalytic asymmetric strategy was developed using unsaturated benzothiophenones and α-nitroketones catalysed by bifunctional squaramide via Michael addition and acyl transfer steps. A broad range of chiral acyloxybenzothiophene derivatives were obtained in good yields (up to 97%) with excellent enantioselectivities (up to 98% ee). What's more, employing different chiral squaramide catalysts and unsaturated benzothiophenones can deliver the acyloxy unit at the 2-position or 3-position of benzothiophene.
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Affiliation(s)
- Cheng Niu
- Key Laboratory of Medical Molecule Science & Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5 Zhongguancun South Street, Beijing 100081, People's Republic of China.
| | - Da-Ming Du
- Key Laboratory of Medical Molecule Science & Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5 Zhongguancun South Street, Beijing 100081, People's Republic of China.
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5
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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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6
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Long N, Le Gresley A, Wren SP. Thiazolidinediones: An In-Depth Study of Their Synthesis and Application to Medicinal Chemistry in the Treatment of Diabetes Mellitus. ChemMedChem 2021; 16:1716-1735. [PMID: 33844475 PMCID: PMC8251912 DOI: 10.1002/cmdc.202100177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 12/25/2022]
Abstract
2,4-Thiazolidinedione (TZD) is a privileged and highly utilised scaffold for the development of pharmaceutically active compounds. This sulfur-containing heterocycle is a versatile pharmacophore that confers a diverse range of pharmacological activities. TZD has been shown to exhibit biological action towards a vast range of targets interesting to medicinal chemists. In this review, we attempt to provide insight into both the historical conventional and the use of novel methodologies to synthesise the TZD core framework. Further to this, synthetic procedures utilised to substitute the TZD molecule at the activated methylene C5 and N3 position are reviewed. Finally, research into developing clinical agents, which act as modulators of peroxisome proliferator-activated receptors gamma (PPARγ), protein tyrosine phosphatase 1B (PTP1B) and aldose reductase 2 (ALR2), are discussed. These are the three most targeted receptors for the treatment of diabetes mellitus (DM).
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Affiliation(s)
- Nathan Long
- Department of Chemical & Pharmaceutical SciencesFaculty of ScienceEngineering & ComputingKingston University LondonPenrhyn RoadSurreyKT1 2EEUK
| | - Adam Le Gresley
- Department of Chemical & Pharmaceutical SciencesFaculty of ScienceEngineering & ComputingKingston University LondonPenrhyn RoadSurreyKT1 2EEUK
| | - Stephen P. Wren
- Department of Chemical & Pharmaceutical SciencesFaculty of ScienceEngineering & ComputingKingston University LondonPenrhyn RoadSurreyKT1 2EEUK
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7
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Suruzhon M, Bodnarchuk MS, Ciancetta A, Viner R, Wall ID, Essex JW. Sensitivity of Binding Free Energy Calculations to Initial Protein Crystal Structure. J Chem Theory Comput 2021; 17:1806-1821. [PMID: 33534995 DOI: 10.1021/acs.jctc.0c00972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Binding free energy calculations using alchemical free energy (AFE) methods are widely considered to be the most rigorous tool in the computational drug discovery arsenal. Despite this, the calculations suffer from accuracy, precision, and reproducibility issues. In this publication, we perform a high-throughput study of more than a thousand AFE calculations, utilizing over 220 μs of total sampling time, on three different protein systems to investigate the impact of the initial crystal structure on the resulting binding free energy values. We also consider the influence of equilibration time and discover that the initial crystal structure can have a significant effect on free energy values obtained at short timescales that can manifest itself as a free energy difference of more than 1 kcal/mol. At longer timescales, these differences are largely overtaken by important rare events, such as torsional ligand motions, typically resulting in a much higher uncertainty in the obtained values. This work emphasizes the importance of rare event sampling and long-timescale dynamics in free energy calculations even for routinely performed alchemical perturbations. We conclude that an optimal protocol should not only concentrate computational resources on achieving convergence in the alchemical coupling parameter (λ) space but also on longer simulations and multiple repeats.
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Affiliation(s)
- Miroslav Suruzhon
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | | | | | - Russell Viner
- Syngenta, Jealott's Hill International Research Centre, Bracknell RG42 6EY, U.K
| | - Ian D Wall
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
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8
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Temml V, Kutil Z. Structure-based molecular modeling in SAR analysis and lead optimization. Comput Struct Biotechnol J 2021; 19:1431-1444. [PMID: 33777339 PMCID: PMC7979990 DOI: 10.1016/j.csbj.2021.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
In silico methods like molecular docking and pharmacophore modeling are established strategies in lead identification. Their successful application for finding new active molecules for a target is reported by a plethora of studies. However, once a potential lead is identified, lead optimization, with the focus on improving potency, selectivity, or pharmacokinetic parameters of a parent compound, is a much more complex task. Even though in silico molecular modeling methods could contribute a lot of time and cost-saving by rationally filtering synthetic optimization options, they are employed less widely in this stage of research. In this review, we highlight studies that have successfully used computer-aided SAR analysis in lead optimization and want to showcase sound methodology and easily accessible in silico tools for this purpose.
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Affiliation(s)
- Veronika Temml
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg, Austria
| | - Zsofia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
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9
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Guterres H, Park SJ, Jiang W, Im W. Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. J Chem Inf Model 2020; 61:535-546. [PMID: 33337877 DOI: 10.1021/acs.jcim.0c01354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.
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Affiliation(s)
- Hugo Guterres
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sang-Jun Park
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wei Jiang
- Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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10
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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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11
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Recent advance on PTP1B inhibitors and their biomedical applications. Eur J Med Chem 2020; 199:112376. [DOI: 10.1016/j.ejmech.2020.112376] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
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12
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Irgashev RA, Demina NS, Rusinov GL. Construction of 2,3-disubstituted benzo[b]thieno[2,3-d]thiophenes and benzo[4,5]selenopheno[3,2-b]thiophenes using the Fiesselmann thiophene synthesis. Org Biomol Chem 2020; 18:3164-3168. [PMID: 32267276 DOI: 10.1039/d0ob00300j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A series of 3-(hetero)aryl-substituted benzo[b]thieno[2,3-d]thiophenes, bearing various electron withdrawing groups at C-2 position of their scaffolds, were obtained using a convenient approach based on the Fiesselmann thiophene synthesis. To realize this strategy, the Friedel-Crafts acylation of (hetero)arenes with easily accessible 3-chlorobenzo[b]thiophene-2-carbonyl chlorides was initially performed to afford 3-chloro-2-(hetero)aroylbenzo[b]thiophenes. The latter ketones were treated either with methyl thioglycolate in the presence of DBU and calcium oxide powder or successively with sodium sulfide, an alkylating agent, containing methylene active component, and also DBU and calcium oxide, to form the desired benzo[b]thieno[2,3-d]thiophene derivatives. In addition, similar benzo[4,5]selenopheno[3,2-b]thiophene derivatives were prepared in the same manner using 3-bromobenzo[b]selenophen-2-yl substrates. The obtained functional derivatives of both benzo[b]thieno[2,3-d]thiophene and benzo[4,5]selenopheno[3,2-b]thiophene are of interest for further elaboration of organic semiconductor materials.
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Affiliation(s)
- Roman A Irgashev
- Postovsky Institute of Organic Synthesis, Ural Division, Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620990, Russia. and Ural Federal University named after the First President of Russia B. N. Yeltsin, Mira Str., 19, Ekaterinburg, 620002, Russia
| | - Nadezhda S Demina
- Postovsky Institute of Organic Synthesis, Ural Division, Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620990, Russia. and Ural Federal University named after the First President of Russia B. N. Yeltsin, Mira Str., 19, Ekaterinburg, 620002, Russia
| | - Gennady L Rusinov
- Postovsky Institute of Organic Synthesis, Ural Division, Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620990, Russia. and Ural Federal University named after the First President of Russia B. N. Yeltsin, Mira Str., 19, Ekaterinburg, 620002, Russia
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13
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Abstract
Tyrosine phosphorylation is a critical component of signal transduction for multicellular organisms, particularly for pathways that regulate cell proliferation and differentiation. While tyrosine kinase inhibitors have become FDA-approved drugs, inhibitors of the other important components of these signaling pathways have been harder to develop. Specifically, direct phosphotyrosine (pTyr) isosteres have been aggressively pursued as inhibitors of Src homology 2 (SH2) domains and protein tyrosine phosphatases (PTPs). Medicinal chemists have produced many classes of peptide and small molecule inhibitors that mimic pTyr. However, balancing affinity with selectivity and cell penetration has made this an extremely difficult space for developing successful clinical candidates. This review will provide a comprehensive picture of the field of pTyr isosteres, from early beginnings to the current state and trajectory. We will also highlight the major protein targets of these medicinal chemistry efforts, the major classes of peptide and small molecule inhibitors that have been developed, and the handful of compounds which have been tested in clinical trials.
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Affiliation(s)
- Robert A Cerulli
- Cellular, Molecular and Developmental Biology Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
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14
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Yang L, Chen F, Gao C, Chen J, Li J, Liu S, Zhang Y, Wang Z, Qian S. Design and synthesis of tricyclic terpenoid derivatives as novel PTP1B inhibitors with improved pharmacological property and in vivo antihyperglycaemic efficacy. J Enzyme Inhib Med Chem 2020; 35:152-164. [PMID: 31742469 PMCID: PMC6882489 DOI: 10.1080/14756366.2019.1690481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Overexpression of protein tyrosine phosphatase 1B (PTP1B) induces insulin resistance in various basic and clinical research. In our previous work, a synthetic oleanolic acid (OA) derivative C10a with PTP1B inhibitory activity has been reported. However, C10a has some pharmacological defects and cytotoxicity. Herein, a structure-based drug design approach was used based on the structure of C10a to elaborate the smaller tricyclic core. A series of tricyclic derivatives were synthesised and the compounds 15, 28 and 34 exhibited the most PTP1B enzymatic inhibitory potency. In the insulin-resistant human hepatoma HepG2 cells, compound 25 with the moderate PTP1B inhibition and preferable pharmaceutical properties can significantly increase insulin-stimulated glucose uptake and showed the insulin resistance ameliorating effect. Moreover, 25 showed the improved in vivo antihyperglycaemic potential in the nicotinamide–streptozotocin-induced T2D. Our study demonstrated that these tricyclic derivatives with improved molecular architectures and antihyperglycaemic activity could be developed in the treatment of T2D.
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Affiliation(s)
- Lingling Yang
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
| | - Feng Chen
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
| | - Cheng Gao
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
| | - Jiabao Chen
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
| | - Junyan Li
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
| | - Siyan Liu
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
| | - Yuanyuan Zhang
- Department of Chemistry, College of Science, Xihua University, Chengdu, China
| | - Zhouyu Wang
- Department of Chemistry, College of Science, Xihua University, Chengdu, China
| | - Shan Qian
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, China
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15
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Panigrahi K, Fei X, Kitamura M, Berkowitz DB. Rapid Entry into Biologically Relevant α,α-Difluoroalkylphosphonates Bearing Allyl Protection-Deblocking under Ru(II)/(IV)-Catalysis. Org Lett 2019; 21:9846-9851. [PMID: 31789041 DOI: 10.1021/acs.orglett.9b03707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A convenient synthetic route to α,α-difluoroalkylphosphonates is described. Structurally diverse aldehydes are condensed with LiF2CP(O)(OCH2CH═CH2)2. The resultant alcohols are captured as the pentafluorophenyl thionocarbonates and efficiently deoxygenated with HSnBu3, BEt3, and O2, and then smoothly deblocked with CpRu(IV)(π-allyl)quinoline-2-carboxylate (1-2 mol %) in methanol as an allyl cation scavenger. These mild deprotection conditions provide access to free α,α-difluoroalkylphosphonates in nearly quantitative yield. This methodology is used to rapidly construct new bis-α,α-difluoroalkyl phosphonate inhibitors of PTPIB (protein phosphotyrosine phosphatase-1B).
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Affiliation(s)
- Kaushik Panigrahi
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Xiang Fei
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Masato Kitamura
- Graduate School of Pharmaceutical Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - David B Berkowitz
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
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16
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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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18
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Molecular Dynamics Simulations of A27S and K120A Mutated PTP1B Reveals Selective Binding of the Bidentate Inhibitor. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9852897. [PMID: 30729132 PMCID: PMC6341276 DOI: 10.1155/2019/9852897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/09/2018] [Accepted: 12/24/2018] [Indexed: 11/26/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is considered a potential target for the treatment of type II diabetes and obesity due to its critical negative role in the insulin signaling pathway. However, improving the selectivity of PTP1B inhibitors over the most closely related T-cell protein tyrosine phosphatase (TCPTP) remains a major challenge for inhibitor development. Lys120 at the active site and Ser27 at the second pTyr binding site are distinct in PTP1B and TCPTP, which may bring differences in binding affinity. To explore the determinant of selective binding of inhibitor, molecular dynamics simulations with binding free energy calculations were performed on K120A and A27S mutated PTP1B, and the internal changes induced by mutations were investigated. Results reveal that the presence of Lys120 induces a conformational change in the WPD-loop and YRD-motif and has a certain effect on the selective binding at the active site. Ser27 weakens the stability of the inhibitor at the second pTyr binding site by altering the orientation of the Arg24 and Arg254 side chains via hydrogen bonds. Further comparison of alanine scanning demonstrates that the reduction in the energy contribution of Arg254 caused by A27S mutation leads to a different inhibitory activity. These observations provide novel insights into the selective binding mechanism of PTP1B inhibitors to TCPTP.
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19
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Zhao C, Rakesh KP, Ravidar L, Fang WY, Qin HL. Pharmaceutical and medicinal significance of sulfur (S VI)-Containing motifs for drug discovery: A critical review. Eur J Med Chem 2019; 162:679-734. [PMID: 30496988 PMCID: PMC7111228 DOI: 10.1016/j.ejmech.2018.11.017] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/17/2018] [Accepted: 11/07/2018] [Indexed: 01/04/2023]
Abstract
Sulfur (SVI) based moieties, especially, the sulfonyl or sulfonamide based analogues have showed a variety of pharmacological properties, and its derivatives propose a high degree of structural diversity that has established useful for the finding of new therapeutic agents. The developments of new less toxic, low cost and highly active sulfonamides containing analogues are hot research topics in medicinal chemistry. Currently, more than 150 FDA approved Sulfur (SVI)-based drugs are available in the market, and they are widely used to treat various types of diseases with therapeutic power. This comprehensive review highlights the recent developments of sulfonyl or sulfonamides based compounds in huge range of therapeutic applications such as antimicrobial, anti-inflammatory, antiviral, anticonvulsant, antitubercular, antidiabetic, antileishmanial, carbonic anhydrase, antimalarial, anticancer and other medicinal agents. We believe that, this review article is useful to inspire new ideas for structural design and developments of less toxic and powerful Sulfur (SVI) based drugs against the numerous death-causing diseases.
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Affiliation(s)
- Chuang Zhao
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China
| | - K P Rakesh
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China.
| | - L Ravidar
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China
| | - Wan-Yin Fang
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China
| | - Hua-Li Qin
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China.
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20
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Morishita K, Shoji Y, Fukui M, Ito Y, Kitao T, Ozawa SI, Hirono S, Shirahase H. 2-Acyl-3-carboxyl-tetrahydroisoquinoline Derivatives: Mixed-Type PTP1B Inhibitors without PPARγ Activation. Chem Pharm Bull (Tokyo) 2018; 66:1131-1152. [DOI: 10.1248/cpb.c18-00571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ko Morishita
- Drug Discovery Research Department, Kyoto Pharmaceutical Industries, Ltd
| | - Yoshimichi Shoji
- Drug Discovery Research Department, Kyoto Pharmaceutical Industries, Ltd
| | - Masaki Fukui
- Drug Discovery Research Department, Kyoto Pharmaceutical Industries, Ltd
| | - Yuma Ito
- Drug Discovery Research Department, Kyoto Pharmaceutical Industries, Ltd
| | - Tatsuya Kitao
- Drug Discovery Research Department, Kyoto Pharmaceutical Industries, Ltd
| | | | | | - Hiroaki Shirahase
- Drug Discovery Research Department, Kyoto Pharmaceutical Industries, Ltd
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21
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Chen X, Gan Q, Feng C, Liu X, Zhang Q. Investigation of selective binding of inhibitors to PTP1B and TCPTP by accelerated molecular dynamics simulations. J Biomol Struct Dyn 2018; 37:3697-3706. [DOI: 10.1080/07391102.2018.1526117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xi Chen
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Qiang Gan
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Changgen Feng
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Xia Liu
- College of Science, China Agricultural University, Beijing, China
| | - Qian Zhang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China
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22
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Computational Insight into Protein Tyrosine Phosphatase 1B Inhibition: A Case Study of the Combined Ligand- and Structure-Based Approach. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:4245613. [PMID: 29441120 PMCID: PMC5758944 DOI: 10.1155/2017/4245613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an attractive target for treating cancer, obesity, and type 2 diabetes. In our work, the way of combined ligand- and structure-based approach was applied to analyze the characteristics of PTP1B enzyme and its interaction with competitive inhibitors. Firstly, the pharmacophore model of PTP1B inhibitors was built based on the common feature of sixteen compounds. It was found that the pharmacophore model consisted of five chemical features: one aromatic ring (R) region, two hydrophobic (H) groups, and two hydrogen bond acceptors (A). To further elucidate the binding modes of these inhibitors with PTP1B active sites, four docking programs (AutoDock 4.0, AutoDock Vina 1.0, standard precision (SP) Glide 9.7, and extra precision (XP) Glide 9.7) were used. The characteristics of the active sites were then described by the conformations of the docking results. In conclusion, a combination of various pharmacophore features and the integration information of structure activity relationship (SAR) can be used to design novel potent PTP1B inhibitors.
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23
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Gulipalli KC, Bodige S, Ravula P, Endoori S, Vanaja GR, Suresh Babu G, Narendra Sharath Chandra JN, Seelam N. Design, synthesis, in silico and in vitro evaluation of thiophene derivatives: A potent tyrosine phosphatase 1B inhibitor and anticancer activity. Bioorg Med Chem Lett 2017; 27:3558-3564. [PMID: 28579122 DOI: 10.1016/j.bmcl.2017.05.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/06/2017] [Accepted: 05/16/2017] [Indexed: 11/24/2022]
Abstract
A series of novel methyl 4-(4-amidoaryl)-3-methoxythiophene-2-carboxylate derivatives were designed against the active site of protein tyrosine phosphatise 1B (PTP1B) enzyme using MOE.2008.10. These molecules are also subjected for in silico toxicity prediction studies and considering their corresponding drug scores, it implied that, the molecules are promising as anticancer agents. The designed compounds were synthesized by using suitable methods and characterized. They were subjected to inhibitory activity against PTP1B and in vitro anticancer activity by MTT assay. Most of the tested compounds showed potent inhibitory activity against PTP1B, among the compounds tested, compound 5b exhibited the highest activity (IC50=5.25µM) and remarkable cytotoxic activity at 0.09µM of IC50 against the MCF-7 cell line. In addition to this, compound 5c also showed potential anticancer activity at 2.22µM of IC50 against MCF-7 and 0.72µM against HepG2 cell lines as well as PTP1B inhibitory activity at IC50 of 6.37µM.
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Affiliation(s)
- Kali Charan Gulipalli
- Department of Chemistry, K L University, Green Fields, Vaddeswaram, Guntur 522502, India
| | - Srinu Bodige
- Department of Chemistry, K L University, Green Fields, Vaddeswaram, Guntur 522502, India
| | - Parameshwar Ravula
- Department of Pharmaceutical Chemistry, Gurunanak Institutions Technical Campus, School of Pharmacy, Hyderabad, India
| | - Srinivas Endoori
- Department of Chemistry, K L University, Green Fields, Vaddeswaram, Guntur 522502, India
| | - G R Vanaja
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, India
| | - G Suresh Babu
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, India
| | | | - Nareshvarma Seelam
- Department of Chemistry, K L University, Green Fields, Vaddeswaram, Guntur 522502, India.
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Mahapatra MK, Kumar R, Kumar M. N-alkylated thiazolidine-2,4-dione analogs as PTP1B inhibitors: synthesis, biological activity, and docking studies. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1823-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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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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27
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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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Synthesis of some new Thieno[2,3-b]pyridines, Pyrimidino[4',5':4,5]thieno[2,3-b]pyridine and Pyridines Incorporating 5-Bromobenzofuran-2-yl Moiety. Molecules 2015; 20:822-38. [PMID: 25574823 PMCID: PMC6272347 DOI: 10.3390/molecules20010822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 12/29/2014] [Indexed: 02/02/2023] Open
Abstract
2-Sulfanyl-6-(2-thienyl)pyridine-3-carbonitrile, 1-Amino-6-(5-bromo-benzofuran-2-yl)-2-oxo-1,2-dihydro-pyridine-3-carbonitrile, thieno[2,3-b]pyridins, pyrimidino[4',5':4,5]thieno[2,3-b]pyridine, quinazoline and carbamate derivatives were synthesized from sodium 3-(5-bromobenzofuran-2-yl)-3-oxoprop-1-en-1-olate with. The newly synthesized compounds were elucidated by elemental analysis, spectral data, and alternative synthesis whenever possible and chemical transportation.
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29
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Kaupang Å, Hildonen S, Halvorsen TG, Mortén M, Vik A, Hansen TV. Involvement of covalent interactions in the mode of action of PPARβ/δ antagonists. RSC Adv 2015. [DOI: 10.1039/c5ra15707b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Investigations on the mode of action of several different chemical modulators of the peroxisome proliferator-activated receptor β/δ (PPARβ/δ) have been reported using MS and NMR experiments.
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Affiliation(s)
- Åsmund Kaupang
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | - Siri Hildonen
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | - Trine G. Halvorsen
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | - Magnus Mortén
- Department of Chemistry
- University of Oslo
- 0315 Oslo
- Norway
| | - Anders Vik
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | - Trond Vidar Hansen
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
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30
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Identification of novel PTP1B inhibitors by pharmacophore based virtual screening, scaffold hopping and docking. Eur J Med Chem 2014; 87:578-94. [DOI: 10.1016/j.ejmech.2014.09.097] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/23/2022]
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31
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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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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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Matloubi Moghaddam F, Khodabakhshi MR, Latifkar A. A one-pot multicomponent synthesis of polysubstituted thiophenes via the reactions of an isocyanide, α-haloketones, and β-ketodithioesters in water. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Design, synthesis and molecular modelling studies of novel 3-acetamido-4-methyl benzoic acid derivatives as inhibitors of protein tyrosine phosphatase 1B. Eur J Med Chem 2013; 70:469-76. [DOI: 10.1016/j.ejmech.2013.10.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/20/2022]
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35
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In silico accounting of novel pyridazine analogues as h-PTP 1B inhibitors: pharmacophore modelling, atom-based 3D QSAR and docking studies. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0797-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Baguley TD, Xu HC, Chatterjee M, Nairn AC, Lombroso PJ, Ellman JA. Substrate-based fragment identification for the development of selective, nonpeptidic inhibitors of striatal-enriched protein tyrosine phosphatase. J Med Chem 2013; 56:7636-50. [PMID: 24083656 DOI: 10.1021/jm401037h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High levels of striatal-enriched protein tyrosine phosphatase (STEP) activity are observed in a number of neuropsychiatric disorders such as Alzheimer's disease. Overexpression of STEP results in the dephosphorylation and inactivation of many key neuronal signaling molecules, including ionotropic glutamate receptors. Moreover, genetically reducing STEP levels in AD mouse models significantly reversed cognitive deficits and decreased glutamate receptor internalization. These results support STEP as a potential target for drug discovery for the treatment of Alzheimer's disease. Herein, a substrate-based approach for the discovery and optimization of fragments called substrate activity screening (SAS) has been applied to the development of low molecular weight (<450 Da) and nonpeptidic, single-digit micromolar mechanism-based STEP inhibitors with greater than 20-fold selectivity across multiple tyrosine and dual specificity phosphatases. Significant levels of STEP inhibition in rat cortical neurons are also observed.
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Affiliation(s)
- Tyler D Baguley
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
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37
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A paradigm for development of novel PTP 1B inhibitors: Pharmacophore modelling, atom-based 3D-QSAR and docking studies. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0690-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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38
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Baskaran SK, Goswami N, Selvaraj S, Muthusamy VS, Lakshmi BS. Molecular Dynamics Approach to Probe the Allosteric Inhibition of PTP1B by Chlorogenic and Cichoric Acid. J Chem Inf Model 2012; 52:2004-12. [DOI: 10.1021/ci200581g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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39
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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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40
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Patel D, Jain M, Shah SR, Bahekar R, Jadav P, Joharapurkar A, Dhanesha N, Shaikh M, Sairam KV, Kapadnis P. Discovery of potent, selective and orally bioavailable triaryl-sulfonamide based PTP1B inhibitors. Bioorg Med Chem Lett 2012; 22:1111-7. [DOI: 10.1016/j.bmcl.2011.11.122] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/11/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
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41
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Sun LP, Shen Q, Piao HH, Ma WP, Gao LX, Zhang W, Nan FJ, Li J, Piao HR. Synthesis and biological evaluation of (±)-3-(2-(2-fluorobenzyloxy) naphthalen-6-yl)-2-aminopropanoic acid derivatives as novel PTP1B inhibitors. Eur J Med Chem 2011; 46:3630-8. [DOI: 10.1016/j.ejmech.2011.05.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022]
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42
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Patel D, Jain M, Shah SR, Bahekar R, Jadav P, Darji B, Siriki Y, Bandyopadhyay D, Joharapurkar A, Kshirsagar S, Patel H, Shaikh M, Sairam KVVM, Patel P. Discovery of Orally Active, Potent, and Selective Benzotriazole-Based PTP1B Inhibitors. ChemMedChem 2011; 6:1011-6. [DOI: 10.1002/cmdc.201100077] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/17/2011] [Indexed: 01/12/2023]
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43
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Qian S, Li H, Chen Y, Zhang W, Yang S, Wu Y. Synthesis and biological evaluation of oleanolic acid derivatives as inhibitors of protein tyrosine phosphatase 1B. JOURNAL OF NATURAL PRODUCTS 2010; 73:1743-1750. [PMID: 20964318 DOI: 10.1021/np100064m] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator in the process of insulin signaling and a promising drug target for diabetes and obesity. Derivatives of oleanolic acid were synthesized and evaluated as PTP1B inhibitors. Several derivatives exhibited moderate to good inhibitory activities against PTP1B, with 25f displaying the most promising inhibition (IC(50) = 3.12 μM). Structure-activity relationship analyses of these derivatives demonstrated that the integrity of the A ring and 12-ene moieties was important in the retention of PTP1B enzyme inhibitory activities. In addition, hydrophilic and acidic groups as well as the distance between the oleanene and acid moieties were associated with PTP1B inhibitory activities. Possible binding modes of 25f were explored by molecular docking simulations.
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Affiliation(s)
- Shan Qian
- Bioengineering College, Xihua University, Chengdu 610039, People's Republic of China
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44
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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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45
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Yesudas JP, Sayyed FB, Suresh CH. Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT. J Mol Model 2010; 17:401-13. [PMID: 20490879 DOI: 10.1007/s00894-010-0736-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 04/27/2010] [Indexed: 11/29/2022]
Abstract
A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously-the structural water-is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L.
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Affiliation(s)
- Joshy P Yesudas
- Computational Modeling and Simulation Section, National Institute for Interdisciplinary Science and Technology (CSIR), Trivandrum, India
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46
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Synthesis, Electrochemical, and Optical Properties of New Fluorescent, Substituted Thieno[3,2-b][1]Benzothiophenes. J Fluoresc 2010; 20:1037-47. [DOI: 10.1007/s10895-010-0656-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2010] [Accepted: 03/26/2010] [Indexed: 11/30/2022]
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47
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Ye D, Zhang Y, Wang F, Zheng M, Zhang X, Luo X, Shen X, Jiang H, Liu H. Novel thiophene derivatives as PTP1B inhibitors with selectivity and cellular activity. Bioorg Med Chem 2010; 18:1773-82. [DOI: 10.1016/j.bmc.2010.01.055] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 01/22/2010] [Indexed: 01/10/2023]
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48
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Vidović D, Schürer SC. Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design. J Med Chem 2009; 52:6649-59. [PMID: 19810703 DOI: 10.1021/jm9008899] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation, controlled by the coordinated action of protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs), is a fundamental regulatory mechanism of numerous physiological processes. PTPs are implicated in a number of human diseases, and their potential as prospective drug targets is increasingly being recognized. Despite their biological importance, until now no comprehensive overview has been reported describing how all members of the human PTP family are related. Here we review the entire human PTP family and present a systematic knowledge-based characterization of global and local similarity relationships, which are relevant for the development of small molecule inhibitors. We use parallel homology modeling to expand the current PTP structure space and analyze the human PTPs based on local three-dimensional catalytic sites and domain sequences. Furthermore, we demonstrate the importance of binding site similarities in understanding cross-reactivity and inhibitor selectivity in the design of small molecule inhibitors.
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Affiliation(s)
- Dusica Vidović
- Center for Computational Science, University of Miami, Miami, Florida 33136, USA
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49
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Erbe DV, Klaman LD, Wilson DP, Wan ZK, Kirincich SJ, Will S, Xu X, Kung L, Wang S, Tam S, Lee J, Tobin JF. Prodrug delivery of novel PTP1B inhibitors to enhance insulin signalling. Diabetes Obes Metab 2009; 11:579-88. [PMID: 19383031 DOI: 10.1111/j.1463-1326.2008.01022.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A growing percentage of the population is resistant to two key hormones - insulin and leptin - as a result of increased obesity, often leading to significant health consequences such as type 2 diabetes. Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of signalling by both of these hormones, so that inhibitors of this enzyme may provide promise for correcting endocrine abnormalities in both diabetes and obesity. As with other tyrosine phosphatases, identification of viable drug candidates targeting PTP1B has been elusive because of the nature of its active site. Beginning with novel phosphotyrosine mimetics, we have designed some of the most potent PTP1B inhibitors. However, their highly acidic structures limit intrinsic permeability and pharmacokinetics. Ester prodrugs of these inhibitors improve their drug-like properties with the goal of delivering these nanomolar inhibitors to the cytoplasm of cells within target tissues. In addition to identifying prodrugs that is able to deliver active drugs into cells to inhibit PTP1B and increase insulin signalling, these compounds were further modified to gain a variety of cleavage properties for targeting activity in vivo. One such prodrug candidate improved insulin sensitivity in ob/ob mice, with lowered fasting blood glucose levels seen in the context of lowered fasting insulin levels following 4 days of intraperitoneal dosing. The results presented in this study highlight the potential for design of orally active drug candidates targeting PTP1B, while also delineating the considerable challenges remaining.
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Affiliation(s)
- D V Erbe
- Departments of Metabolic Diseases and Chemical Sciences, Wyeth Research, Cambridge, MA 02140, USA.
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50
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Brandão TAS, Robinson H, Johnson SJ, Hengge AC. Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures. J Am Chem Soc 2009; 131:778-86. [PMID: 19140798 PMCID: PMC2739089 DOI: 10.1021/ja807418b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 A structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO](2) core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.
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Affiliation(s)
- Tiago A. S. Brandão
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
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