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Dong J, Jassim BA, Milholland KL, Qu Z, Bai Y, Miao Y, Miao J, Ma Y, Lin J, Hall MC, Zhang ZY. Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases. J Med Chem 2024; 67:8817-8835. [PMID: 38768084 DOI: 10.1021/acs.jmedchem.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) control protein tyrosine phosphorylation and regulate numerous cellular functions. Dysregulated PTP activity is associated with the onset of multiple human diseases. Nevertheless, understanding of the physiological function and disease biology of most PTPs remains limited, largely due to the lack of PTP-specific chemical probes. In this study, starting from a well-known nonhydrolyzable phosphotyrosine (pTyr) mimetic, phosphonodifluoromethyl phenylalanine (F2Pmp), we synthesized 7 novel phosphonodifluoromethyl-containing bicyclic/tricyclic aryl derivatives with improved cell permeability and potency toward various PTPs. Furthermore, with fragment- and structure-based design strategies, we advanced compound 9 to compound 15, a first-in-class, potent, selective, and bioavailable inhibitor of human CDC14A and B phosphatases. This study demonstrates the applicability of the fragment-based design strategy in creating potent, selective, and bioavailable PTP inhibitors and provides a valuable probe for interrogating the biological roles of hCDC14 phosphatases and assessing their potential for therapeutic interventions.
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Affiliation(s)
- Jiajun Dong
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brenson A Jassim
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yunpeng Bai
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yiming Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuan Ma
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianping Lin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Gai S, Suthagar K, Shaffer KJ, Jiao W, Minnow YVT, Glockzin K, Maatouk SW, Katzfuss A, Meek TD, Schramm VL, Tyler PC. The design of protozoan phosphoribosyltransferase inhibitors containing non-charged phosphate mimic residues. Bioorg Med Chem 2022; 74:117038. [PMID: 36209571 DOI: 10.1016/j.bmc.2022.117038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 01/11/2023]
Abstract
Phosphate groups play essential roles in biological processes, including retention inside biological membranes. Phosphodiesters link nucleic acids, and the reversible transfer of phosphate groups is essential in energy metabolism and cell-signalling processes. Phosphorylated metabolic intermediates are known targets for metabolic and disease-related disorders, and the enzymes involved in these pathways recognize phosphate groups in their catalytic sites. Therapeutics that target these enzymes can require charged (ionic) entities to capture the binding energy of ionic substrates. Such compounds are not cell-permeable and require pro-drug strategies for efficacy as therapeutics. Protozoan parasites such as Plasmodium and Trypanosoma spp. are unable to synthesise purines de novo and rely on the salvage of purines from the host cell to synthesise free purine bases. Purine phosphoribosyltransfereases (PPRTases) play a crucial role for purine salvage and are potential target for drug development. Here we present attempts to design inhibitors of PPRTases that are non-ionic and show affinity for the nucleotide 5'-phosphate binding site. Inhibitor design was based on known potent ionic inhibitors, reported phosphate mimics and computational modelling studies.
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Affiliation(s)
- Sinan Gai
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Kajitha Suthagar
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Karl J Shaffer
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Wanting Jiao
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Yacoba V T Minnow
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Sean W Maatouk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand.
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Computational Methods in Cooperation with Experimental Approaches to Design Protein Tyrosine Phosphatase 1B Inhibitors in Type 2 Diabetes Drug Design: A Review of the Achievements of This Century. Pharmaceuticals (Basel) 2022; 15:ph15070866. [PMID: 35890163 PMCID: PMC9322956 DOI: 10.3390/ph15070866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) dephosphorylates phosphotyrosine residues and is an important regulator of several signaling pathways, such as insulin, leptin, and the ErbB signaling network, among others. Therefore, this enzyme is considered an attractive target to design new drugs against type 2 diabetes, obesity, and cancer. To date, a wide variety of PTP1B inhibitors that have been developed by experimental and computational approaches. In this review, we summarize the achievements with respect to PTP1B inhibitors discovered by applying computer-assisted drug design methodologies (virtual screening, molecular docking, pharmacophore modeling, and quantitative structure–activity relationships (QSAR)) as the principal strategy, in cooperation with experimental approaches, covering articles published from the beginning of the century until the time this review was submitted, with a focus on studies conducted with the aim of discovering new drugs against type 2 diabetes. This review encourages the use of computational techniques and includes helpful information that increases the knowledge generated to date about PTP1B inhibition, with a positive impact on the route toward obtaining a new drug against type 2 diabetes with PTP1B as a molecular target.
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4
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Jun JJ, Xie X. Implementation of Diverse Synthetic and Strategic Approaches to Biologically Active Sulfamides. ChemistrySelect 2021. [DOI: 10.1002/slct.202004765] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jaden J. Jun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center School of Pharmacy 335 Sutherland Drive 206 Salk Pavilion University of Pittsburgh Pittsburgh PA15261 USA
- NIH National Center of Excellence for Computational Drug Abuse Research
- Drug Discovery Institute
| | - Xiang‐Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center School of Pharmacy 335 Sutherland Drive 206 Salk Pavilion University of Pittsburgh Pittsburgh PA15261 USA
- NIH National Center of Excellence for Computational Drug Abuse Research
- Drug Discovery Institute
- Departments of Computational Biology and Structural Biology Director of CCGS and NIDA CDAR Centers School of Medicine University of Pittsburgh Pittsburgh Pennsylvania 15261 United States
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Yang Y, Tian JY, Ye F, Xiao Z. Identification of natural products as selective PTP1B inhibitors via virtual screening. Bioorg Chem 2020; 98:103706. [PMID: 32199302 DOI: 10.1016/j.bioorg.2020.103706] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/11/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is emerging as a promising yet challenging target for drug discovery. To identify natural products as new prototypes for PTP1B inhibitors, we employed a hierarchical protocol combining ligand-based and structure-based approaches for virtual screening against natural product libraries. Twenty-six compounds were prioritized for enzymatic evaluation against PTP1B, and ten of them were recognized as potent PTP1B inhibitors with IC50 values at the micromolar level. Notably, nine compounds demonstrated evident selectivity to PTP1B over four other PTPs, including the most homologous T-cell protein tyrosine phosphatase (TCPTP). The results implicated that the structural uniqueness of the natural products might be a potential solution to the selectivity issue associated with the target PTP1B.
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Affiliation(s)
- Ying Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jin-Ying Tian
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fei Ye
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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Volatile Secondary Metabolites with Potent Antidiabetic Activity from the Roots of Prangos pabularia Lindl.—Computational and Experimental Investigations. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9112362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
(1) Background: Almost 500 million people worldwide are suffering from diabetes. Since ancient times, humans have used medicinal plants for the treatment of diabetes. Medicinal plants continue to serve as natural sources for the discovery of antidiabetic compounds. Prangos pabularia Lindl. is a widely distributed herb with large reserves in Tajikistan. Its roots and fruits have been used in Tajik traditional medicine. To our best knowledge, there are no previously published reports concerning the antidiabetic activity and the chemical composition of the essential oil obtained from roots of P. pabularia. (2) Methods: The volatile secondary metabolites were obtained by hydrodistillation from the underground parts of P. pabularia growing wild in Tajikistan and were analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). Protein tyrosine phosphatase 1B (PTP-1B) inhibition assay and molecular docking analysis were carried out to evaluate the potential antidiabetic activity of the P. pabularia essential oil. (3) Results: The main constituents of the volatile oil of P. pabularia were 5-pentylcyclohexa-1,3-diene (44.6%), menthone (12.6%), 1-tridecyne (10.9%), and osthole (6.0%). PTP-1B inhibition assay of the essential oil and osthole resulted in significant inhibitory activity with an IC50 value of 0.06 ± 0.01 and 0.93 ± 0.1 μg/mL. Molecular docking analysis suggests volatile compounds such as osthole inhibit PTP-1B, and the results are also in agreement with experimental investigations. (4) Conclusions: Volatile secondary metabolites and the pure isolated compound (osthole) from the roots of P. pabularia exhibited potent antidiabetic activity, twenty-five and nearly two times more than the positive control (3-(3,5-dibromo-4-hydroxybenzoyl)-2-ethylbenzofuran-6-sulfonic acid-(4-(thiazol-2-ylsulfamyl)-phenyl)-amide)) with an IC50 value of 1.46 ± 0.4 μg/mL, respectively.
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Du Y, Zhang Y, Ling H, Li Q, Shen J. Discovery of novel high potent and cellular active ADC type PTP1B inhibitors with selectivity over TC-PTP via modification interacting with C site. Eur J Med Chem 2018; 144:692-700. [DOI: 10.1016/j.ejmech.2017.12.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 09/05/2017] [Accepted: 12/17/2017] [Indexed: 12/12/2022]
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Sarabia-Sánchez MJ, Trejo-Soto PJ, Velázquez-López JM, Carvente-García C, Castillo R, Hernández-Campos A, Avitia-Domínguez C, Enríquez-Mendiola D, Sierra-Campos E, Valdez-Solana M, Salas-Pacheco JM, Téllez-Valencia A. Novel Mixed-Type Inhibitors of Protein Tyrosine Phosphatase 1B. Kinetic and Computational Studies. Molecules 2017; 22:molecules22122262. [PMID: 29261102 PMCID: PMC6150025 DOI: 10.3390/molecules22122262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 11/21/2022] Open
Abstract
The Atlas of Diabetes reports 415 million diabetics in the world, a number that has surpassed in half the expected time the twenty year projection. Type 2 diabetes is the most frequent form of the disease; it is characterized by a defect in the secretion of insulin and a resistance in its target organs. In the search for new antidiabetic drugs, one of the principal strategies consists in promoting the action of insulin. In this sense, attention has been centered in the protein tyrosine phosphatase 1B (PTP1B), a protein whose overexpression or increase of its activity has been related in many studies with insulin resistance. In the present work, a chemical library of 250 compounds was evaluated to determine their inhibition capability on the protein PTP1B. Ten molecules inhibited over the 50% of the activity of the PTP1B, the three most potent molecules were selected for its characterization, reporting Ki values of 5.2, 4.2 and 41.3 µM, for compounds 1, 2, and 3, respectively. Docking and molecular dynamics studies revealed that the three inhibitors made interactions with residues at the secondary binding site to phosphate, exclusive for PTP1B. The data reported here support these compounds as hits for the design more potent and selective inhibitors against PTP1B in the search of new antidiabetic treatment.
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Affiliation(s)
- Marie Jazmín Sarabia-Sánchez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
| | - Pedro Josué Trejo-Soto
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - José Miguel Velázquez-López
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Carlos Carvente-García
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Rafael Castillo
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Alicia Hernández-Campos
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
| | - Daniel Enríquez-Mendiola
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango C.P. 35010, Mexico.
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango C.P. 35010, Mexico.
| | - José Manuel Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Av. Universidad S/N, Durango, Durango C.P. 34000, Mexico.
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
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Punthasee P, Laciak AR, Cummings AH, Ruddraraju KV, Lewis SM, Hillebrand R, Singh H, Tanner JJ, Gates KS. Covalent Allosteric Inactivation of Protein Tyrosine Phosphatase 1B (PTP1B) by an Inhibitor–Electrophile Conjugate. Biochemistry 2017; 56:2051-2060. [DOI: 10.1021/acs.biochem.7b00151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Puminan Punthasee
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Adrian R. Laciak
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Andrea H. Cummings
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | | | - Sarah M. Lewis
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Roman Hillebrand
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Harkewal Singh
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
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Balachandran N, To F, Berti PJ. Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic. Biochemistry 2017; 56:592-601. [PMID: 28045507 DOI: 10.1021/acs.biochem.6b01211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Naresh Balachandran
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Frederick To
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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Balachandran N, Heimhalt M, Liuni P, To F, Wilson DJ, Junop MS, Berti PJ. Potent Inhibition of 3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) Synthase by DAHP Oxime, a Phosphate Group Mimic. Biochemistry 2016; 55:6617-6629. [DOI: 10.1021/acs.biochem.6b00930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Peter Liuni
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | | | - Derek J. Wilson
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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Chandra S, Pandey J, Tamrakar AK, Siddiqi MI. Multiple machine learning based descriptive and predictive workflow for the identification of potential PTP1B inhibitors. J Mol Graph Model 2016; 71:242-256. [PMID: 28006676 DOI: 10.1016/j.jmgm.2016.10.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/27/2016] [Accepted: 10/25/2016] [Indexed: 12/21/2022]
Abstract
In insulin and leptin signaling pathway, Protein-Tyrosine Phosphatase 1B (PTP1B) plays a crucial controlling role as a negative regulator, which makes it an attractive therapeutic target for both Type-2 Diabetes (T2D) and obesity. In this work, we have generated classification models by using the inhibition data set of known PTP1B inhibitors to identify new inhibitors of PTP1B utilizing multiple machine learning techniques like naïve Bayesian, random forest, support vector machine and k-nearest neighbors, along with structural fingerprints and selected molecular descriptors. Several models from each algorithm have been constructed and optimized, with the different combination of molecular descriptors and structural fingerprints. For the training and test sets, most of the predictive models showed more than 90% of overall prediction accuracies. The best model was obtained with support vector machine approach and has Matthews Correlation Coefficient of 0.82 for the external test set, which was further employed for the virtual screening of Maybridge small compound database. Five compounds were subsequently selected for experimental assay. Out of these two compounds were found to inhibit PTP1B with significant inhibitory activity in in-vitro inhibition assay. The structural fragments which are important for PTP1B inhibition were identified by naïve Bayesian method and can be further exploited to design new molecules around the identified scaffolds. The descriptive and predictive modeling strategy applied in this study is capable of identifying PTP1B inhibitors from the large compound libraries.
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Affiliation(s)
- Sharat Chandra
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Resaerch Institute, Campus, Lucknow 226031, India; Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Jyotsana Pandey
- Biochemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | | | - Mohammad Imran Siddiqi
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Resaerch Institute, Campus, Lucknow 226031, India; Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
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Seridi S, Dinar K, Seridi A, Berredjem M, Kadri M. Charge transfer complexes of 4-isopropyl-2-benzyl-1,2,5-thiadiazolidin-3-one1,1-dioxide with DDQ and TCNE: experimental and DFT studies. NEW J CHEM 2016. [DOI: 10.1039/c5nj03017j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the interaction between sulfahydantoin and two acceptors (DDQ and TCNE) in the liquid phase and in the solid state.
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Affiliation(s)
- Saida Seridi
- Laboratoire de Chimie Physique
- Guelma 24000
- Algeria
| | - Karim Dinar
- Laboratoire de Chimie Physique
- Guelma 24000
- Algeria
| | | | - Malika Berredjem
- Laboratoire de Chimie Organique Appliquée
- Groupe de Chimie Bioorganique
- Université Badji-Mokhtar
- Annaba
- Algeria
| | - Mekki Kadri
- Laboratoire de Chimie Physique
- Guelma 24000
- Algeria
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14
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Ruddraraju KV, Hillebrand R, Barnes CL, Gates KS. Crystal structure of 5-{4'-[(2-{2-[2-(2-ammonio-eth-oxy)eth-oxy]eth-oxy}eth-yl)carbamo-yl]-4-meth-oxy-[1,1'-biphen-yl]-3-yl}-3-oxo-1,2,5-thia-diazo-lidin-2-ide 1,1-dioxide: a potential inhibitor of the enzyme protein tyrosine phosphatase 1B (PTP1B). Acta Crystallogr E Crystallogr Commun 2015; 71:336-8. [PMID: 26029383 PMCID: PMC4438830 DOI: 10.1107/s2056989015003850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 02/24/2015] [Indexed: 11/10/2022]
Abstract
The title compound, C24H32N4O8S, (I), crystallizes as a zwitterion. The terminal amine N atom of the [(2-{2-[2-(2-ammonio-eth-oxy)eth-oxy]eth-oxy}eth-yl)carbamo-yl] side chain is protonated, while the 1,2,5-thia-diazo-lidin-3-one 1,1-dioxide N atom is deprotonated. The side chain is turned over on itself with an intra-molecular N-H⋯O hydrogen bond. The 1,2,5-thia-diazo-lidin-3-one 1,1-dioxide ring has an envelope conformation with the aryl-substituted N atom as the flap. Its mean plane is inclined by 62.87 (8)° to the aryl ring to which it is attached, while the aryl rings of the biphenyl unit are inclined to one another by 20.81 (8)°. In the crystal, mol-ecules are linked by N-H⋯O and N-H⋯N hydrogen bonds, forming slabs lying parallel to (010). Within the slabs there are C-H⋯O and C-H⋯N hydrogen bonds and C-H⋯π inter-actions present.
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Affiliation(s)
| | - Roman Hillebrand
- 125 Chemistry Bldg, University of Missouri Columbia, MO 65211, USA
| | | | - Kent S. Gates
- 125 Chemistry Bldg, University of Missouri Columbia, MO 65211, USA
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15
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Ligand efficiency metrics considered harmful. J Comput Aided Mol Des 2014; 28:699-710. [DOI: 10.1007/s10822-014-9757-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
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16
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Sanchini S, Perruccio F, Piizzi G. Rational Design, Synthesis and Biological Evaluation of Modular Fluorogenic Substrates with High Affinity and Selectivity for PTP1B. Chembiochem 2014; 15:961-76. [DOI: 10.1002/cbic.201400033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Indexed: 11/09/2022]
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17
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Kenny PW, Newman J, Peat TS. Nitrate in the active site of protein tyrosine phosphatase 1B is a putative mimetic of the transition state. ACTA ACUST UNITED AC 2014; 70:565-71. [PMID: 24531490 DOI: 10.1107/s1399004713031052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/12/2013] [Indexed: 11/10/2022]
Abstract
The X-ray crystal structure of the complex of protein tyrosine phosphatase 1B with nitrate anion has been determined and modelled quantum-mechanically. Two protomers were present in the structure, one with the mechanistically important WPD loop closed and the other with this loop open. Nitrate was observed bound to each protomer, making close contacts with the S atom of the catalytic cysteine and a tyrosine residue from a crystallographically related protomer.
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Affiliation(s)
- Peter W Kenny
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S Peat
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
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18
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Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the leptin and insulin signaling pathways. The important roles of PTP1B related to obesity and diabetes were confirmed by a deletion of PTP1B gene in mice. Mice with the whole body deletion of PTP1B were protected against the development of obesity and diabetes. When PTP1B gene was deleted selectively in the brain of mice, the major effects on weight and glucose control were consistent with the whole body deletion of PTP1B. This is in contrast to the muscle-, liver-, and adipocyte-specific deletion, which had no beneficial effects on obesity. While these results indicate the importance of neuronal PTP1B in maintaining energy homeostasis, the peripheral PTP1B is also being investigated for their potential roles in the control of energy balance. Validation of PTP1B as a therapeutic target for obesity and diabetes prompted efforts to develop potent and selective inhibitors of PTP1B. Among the small molecule inhibitors investigated, trodusquemine, which acts both centrally and peripherally, is currently in phase 2 clinical trials. An approach using PTP1B-directed antisense oligonucleotides is also in phase 2 clinical trials.
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Affiliation(s)
- Hyeongjin Cho
- Department of Chemistry, Inha University, Incheon, Korea.
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19
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Larsson EA, Jansson A, Ng FM, Then SW, Panicker R, Liu B, Sangthongpitag K, Pendharkar V, Tai SJ, Hill J, Dan C, Ho SY, Cheong WW, Poulsen A, Blanchard S, Lin GR, Alam J, Keller TH, Nordlund P. Fragment-based ligand design of novel potent inhibitors of tankyrases. J Med Chem 2013; 56:4497-508. [PMID: 23672613 DOI: 10.1021/jm400211f] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Tankyrases constitute potential drug targets for cancer and myelin-degrading diseases. We have applied a structure- and biophysics-driven fragment-based ligand design strategy to discover a novel family of potent inhibitors for human tankyrases. Biophysical screening based on a thermal shift assay identified highly efficient fragments binding in the nicotinamide-binding site, a local hot spot for fragment binding. Evolution of the fragment hit 4-methyl-1,2-dihydroquinolin-2-one (2) along its 7-vector yields dramatic affinity improvements in the first cycle of expansion. A crystal structure of 7-(2-fluorophenyl)-4-methylquinolin-2(1H)-one (11) reveals that the nonplanar compound extends with its fluorine atom into a pocket, which coincides with a region of the active site where structural differences are seen between tankyrases and other poly(ADP-ribose) polymerase (PARP) family members. A further cycle of optimization yielded compounds with affinities and IC50 values in the low nanomolar range and with good solubility, PARP selectivity, and ligand efficiency.
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Affiliation(s)
- E Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, Lab 07-01, 61 Biopolis Drive (Proteos), Singapore 138673.
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20
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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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21
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Boyd SM, Turnbull AP, Walse B. Fragment library design considerations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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22
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Varshney K, Gupta S, Rahuja N, Rawat AK, Singh N, Tamarkar AK, Srivastava AK, Saxena AK. Synthesis, Structure-Activity Relationship and Docking Studies of Substituted Aryl Thiazolyl Phenylsulfonamides as Potential Protein Tyrosine Phosphatase 1B Inhibitors. ChemMedChem 2012; 7:1185-90. [DOI: 10.1002/cmdc.201200197] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Indexed: 11/09/2022]
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23
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Elliott TS, Slowey A, Ye Y, Conway SJ. The use of phosphate bioisosteres in medicinal chemistry and chemical biology. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20079a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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24
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Schwizer D, Patton JT, Cutting B, Smieško M, Wagner B, Kato A, Weckerle C, Binder FPC, Rabbani S, Schwardt O, Magnani JL, Ernst B. Pre-organization of the core structure of E-selectin antagonists. Chemistry 2011; 18:1342-51. [PMID: 22213563 DOI: 10.1002/chem.201102884] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 11/09/2022]
Abstract
A new class of N-acetyl-D-glucosamine (GlcNAc) mimics for E-selectin antagonists was designed and synthesized. The mimic consists of a cyclohexane ring substituted with alkyl substituents adjacent to the linking position of the fucose moiety. Incorporation into E-selectin antagonists led to the test compounds 8 and the 2'-benzoylated analogues 21, which exhibit affinities in the low micromolar range. By using saturation transfer difference (STD)-NMR it could be shown that the increase in affinity does not result from an additional hydrophobic contact of the alkyl substituent with the target protein E-selectin, but rather from a steric effect stabilizing the antagonist in its bioactive conformation. The loss of affinity found for antagonists 10 and 35 containing a methyl substituent in a remote position (and therefore unable to support to the stabilization of the core) further supports this hypothesis. Finally, when a GlcNAc mimetic containing two methyl substituents (52 and 53) was used, in which one methyl was positioned adjacent to the fucose linking position and the other was in a remote position, the affinity was regained.
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Affiliation(s)
- Daniel Schwizer
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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25
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Using small molecules to target protein phosphatases. Bioorg Med Chem 2011; 19:2145-55. [DOI: 10.1016/j.bmc.2011.02.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/21/2011] [Accepted: 02/23/2011] [Indexed: 11/21/2022]
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26
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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27
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Edfeldt FNB, Folmer RHA, Breeze AL. Fragment screening to predict druggability (ligandability) and lead discovery success. Drug Discov Today 2011; 16:284-7. [PMID: 21315179 DOI: 10.1016/j.drudis.2011.02.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/30/2010] [Accepted: 02/02/2011] [Indexed: 10/18/2022]
Affiliation(s)
- Fredrik N B Edfeldt
- Discovery-Enabling Capabilities and Sciences, AstraZeneca R&D, S-43183 Mölndal, Sweden.
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28
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Boettcher A, Ruedisser S, Erbel P, Vinzenz D, Schiering N, Hassiepen U, Rigollier P, Mayr LM, Woelcke J. Fragment-Based Screening by Biochemical Assays. ACTA ACUST UNITED AC 2010; 15:1029-41. [DOI: 10.1177/1087057110380455] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based screening (FBS) has gained acceptance in the pharmaceutical industry as an attractive approach for the identification of new chemical starting points for drug discovery programs in addition to classical strategies such as high-throughput screening. There is the concern that screening of fragments at high µM concentrations in biochemical assays results in increased false-positive and false-negative rates. Here the authors systematically compare the data quality of FBS obtained by enzyme activity-based fluorescence intensity, fluorescence lifetime, and mobility shift assays with the data quality from surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR) methods. The serine protease trypsin and the matrix metalloprotease MMP12 were selected as model systems. For both studies, 352 fragments were selected each. From the data generated, all 3 biochemical protease assay methods can be used for screening of fragments with low false-negative and low false-positive rates, comparable to those achieved with the SPR-based assays. It can also be concluded that only fragments with a solubility higher than the screening concentration determined by means of NMR should be used for FBS purposes. Extrapolated to 10,000 fragments, the biochemical assays speed up the primary FBS process by approximately a factor of 10 and reduce the protease consumption by approximately 10,000-fold compared to NMR protein observation experiments.
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Affiliation(s)
- Andreas Boettcher
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Simon Ruedisser
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Paulus Erbel
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Daniela Vinzenz
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Pascal Rigollier
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Lorenz M. Mayr
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Julian Woelcke
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
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29
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Leone M, Barile E, Vazquez J, Mei A, Guiney D, Dahl R, Pellecchia M. NMR-based design and evaluation of novel bidentate inhibitors of the protein tyrosine phosphatase YopH. Chem Biol Drug Des 2010; 76:10-6. [PMID: 20456369 PMCID: PMC2905849 DOI: 10.1111/j.1747-0285.2010.00982.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We describe the use of a furanyl salicyl nitroxide derivative ('spin-labeled' compound), as a paramagnetic phosphotyrosine mimetic, to carry out a second-site screening by NMR against the PTPase YopH from Yersinia pestis. Using such a fragment-based screening approach we identified several small molecules targeting YopH that bind at sites adjacent to the spin-labeled compound. These second-site fragments were subsequently used to design and synthesize bidentate YopH inhibitors with submicromolar in vitro inhibition, selectivity against the human PTPase PTP1B, and cellular activity against Y. pseudotuberculosis. These initial compounds could result useful in elucidating the structural determinants necessary for YopH inhibition and may help in the design of even more active, selective and cell permeable compounds for the development of novel therapies against Yersiniae.
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Affiliation(s)
- Marilisa Leone
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Elisa Barile
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Jesus Vazquez
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Angel Mei
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Donald Guiney
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Russel Dahl
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Maurizio Pellecchia
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
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30
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Combs AP. Recent Advances in the Discovery of Competitive Protein Tyrosine Phosphatase 1B Inhibitors for the Treatment of Diabetes, Obesity, and Cancer. J Med Chem 2009; 53:2333-44. [DOI: 10.1021/jm901090b] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew P. Combs
- Incyte Corporation, Experimental Station, E336/131A, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
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31
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Ramensky V, Sobol A, Zaitseva N, Rubinov A, Zosimov V. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 2009; 69:349-57. [PMID: 17623865 DOI: 10.1002/prot.21487] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We present a novel notion of binding site local similarity based on the analysis of complete protein environments of ligand fragments. Comparison of a query protein binding site (target) against the 3D structure of another protein (analog) in complex with a ligand enables ligand fragments from the analog complex to be transferred to positions in the target site, so that the complete protein environments of the fragment and its image are similar. The revealed environments are similarity regions and the fragments transferred to the target site are considered as binding patterns. The set of such binding patterns derived from a database of analog complexes forms a cloud-like structure (fragment cloud), which is a powerful tool for computational drug design. It has been shown on independent test sets that the combined use of a traditional energy-based score together with the cloud-based score responsible for the quality of embedding of a ligand into the fragment cloud improves the self-docking and screening results dramatically. The usage of a fragment cloud as a source of positioned molecular fragments fitting the binding protein environment has been validated by reproduction of experimental ligand optimization results.
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32
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Kosugi T, Nakanishi I, Kitaura K. Binding free energy calculations of adenosine deaminase inhibitor and the effect of methyl substitution in inhibitors. J Chem Inf Model 2009; 49:615-22. [PMID: 19243169 DOI: 10.1021/ci8002667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding affinity of an inhibitor is often improved ten times or more by introducing a simple substituent, such as a methyl group or a chlorine atom. We have investigated this phenomenon in the case of adenosine deaminase (ADA) inhibitors using molecular dynamics (MD) simulations and binding free energy calculations, by the linear interaction energy (LIE) method. For MD simulations, the coordination bond parameters and partial charges of atoms around the zinc ion in ADA have been determined by referring to ab initio MO calculations. The calculated binding free energies for seven inhibitors agreed well with the experimental ones, with a maximum error of 1.2 kcal/mol. The effect of methyl substitution in inhibitor molecules was examined on the basis of MD trajectories. It is suggested that the increase in binding affinity is caused by both van der Waals stabilizations by amino acid residues in contact with the introduced methyl group and through favored overall interactions with surrounding residues in the binding pocket.
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Affiliation(s)
- Takahiro Kosugi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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33
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Asaad N, Bethel PA, Coulson MD, Dawson JE, Ford SJ, Gerhardt S, Grist M, Hamlin GA, James MJ, Jones EV, Karoutchi GI, Kenny PW, Morley AD, Oldham K, Rankine N, Ryan D, Wells SL, Wood L, Augustin M, Krapp S, Simader H, Steinbacher S. Dipeptidyl nitrile inhibitors of Cathepsin L. Bioorg Med Chem Lett 2009; 19:4280-3. [PMID: 19515558 DOI: 10.1016/j.bmcl.2009.05.071] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 05/20/2009] [Accepted: 05/21/2009] [Indexed: 10/20/2022]
Abstract
A series of potent Cathepsin L inhibitors with good selectivity with respect to other cysteine Cathepsins is described and SAR is discussed with reference to the crystal structure of a protein-ligand complex.
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Affiliation(s)
- Nabil Asaad
- Respiratory & Inflammation Research Area, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, UK
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34
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5,6-Diarylanthranilo-1,3-dinitriles as a new class of antihyperglycemic agents. Bioorg Med Chem Lett 2009; 19:2158-61. [DOI: 10.1016/j.bmcl.2009.02.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 01/20/2009] [Accepted: 02/27/2009] [Indexed: 11/19/2022]
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35
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Blomberg N, Cosgrove DA, Kenny PW, Kolmodin K. Design of compound libraries for fragment screening. J Comput Aided Mol Des 2009; 23:513-25. [DOI: 10.1007/s10822-009-9264-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 02/16/2009] [Indexed: 01/15/2023]
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36
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Activated sulfahydantoin as Boc-glycine enolate equivalent: highly diastereoselective α-hydroxyalkylation and application to the synthesis of aldopentonate analogues. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2008.12.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Abstract
Protein tyrosine phosphorylation plays a major role in cellular signaling. The level of tyrosine phosphorylation is controlled by protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Disturbance of the normal balance between PTK and PTP activity results in aberrant tyrosine phosphorylation, which has been linked to the etiology of several human diseases, including cancer. A number of PTPs have been implicated in oncogenesis and tumor progression and therefore are potential drug targets for cancer chemotherapy. These include PTP1B, which may augment signaling downstream of HER2/Neu; SHP2, which is the first oncogene in the PTP superfamily and is essential for growth factor-mediated signaling; the Cdc25 phosphatases, which are positive regulators of cell cycle progression; and the phosphatase of regenerating liver (PRL) phosphatases, which promote tumor metastases. As PTPs have emerged as drug targets for cancer, a number of strategies are currently been explored for the identification of various classes of PTP inhibitors. These efforts have resulted many potent, and in some cases selective, inhibitors for PTP1B, SHP2, Cdc25 and PRL phosphatases. Structural information derived from these compounds serves as a solid foundation upon which novel anti-cancer agents targeted to these PTPs can be developed.
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38
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39
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Bharatham K, Bharatham N, Lee KW. Pharmacophore modeling for protein tyrosine phosphatase 1B inhibitors. Arch Pharm Res 2007; 30:533-42. [PMID: 17615669 DOI: 10.1007/bf02977644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A three dimensional chemical feature based pharmacophore model was developed for the inhibitors of protein tyrosine phosphatase 1B (PTP1B) using the CATALYST software, which would provide useful knowledge for performing virtual screening to identify new inhibitors targeted toward type II diabetes and obesity. A dataset of 27 inhibitors, with diverse structural properties, and activities ranging from 0.026 to 600 microM, was selected as a training set. Hypol, the most reliable quantitative four featured pharmacophore hypothesis, was generated from a training set composed of compounds with two H-bond acceptors, one hydrophobic aromatic and one ring aromatic features. It has a correlation coefficient, RMSD and cost difference (null cost-total cost) of 0.946, 0.840 and 65.731, respectively. The best hypothesis (Hypol) was validated using four different methods. Firstly, a cross validation was performed by randomizing the data using the Cat-Scramble technique. The results confirmed that the pharmacophore models generated from the training set were valid. Secondly, a test set of 281 molecules was scored, with a correlation of 0.882 obtained between the experimental and predicted activities. Hypol performed well in correctly discriminating the active and inactive molecules. Thirdly, the model was investigated by mapping on two PTP1B inhibitors identified by different pharmaceutical companies. The Hypol model correctly predicted these compounds as being highly active. Finally, docking simulations were performed on few compounds to substantiate the role of the pharmacophore features at the binding site of the protein by analyzing their binding conformations. These multiple validation approaches provided confidence in the utility of this pharmacophore model as a 3D query for virtual screening to retrieve new chemical entities showing potential as potent PTP1B inhibitors.
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Affiliation(s)
- Kavitha Bharatham
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center Gyeongsang National University, Jinju 660-701 Korea
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40
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Wan ZK, Follows B, Kirincich S, Wilson D, Binnun E, Xu W, Joseph-McCarthy D, Wu J, Smith M, Zhang YL, Tam M, Erbe D, Tam S, Saiah E, Lee J. Probing acid replacements of thiophene PTP1B inhibitors. Bioorg Med Chem Lett 2007; 17:2913-20. [PMID: 17336064 DOI: 10.1016/j.bmcl.2007.02.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 02/15/2007] [Accepted: 02/16/2007] [Indexed: 11/23/2022]
Abstract
The following account describes our systematic effort to replace one of the carboxylate groups of our diacid thiophene PTP1B inhibitors. Active hits were validated using enzymatic assays before pursuing efforts to improve the potency. Only when the C2 carboxylic acid was replaced with another ionizable functional group was reversible and competitive inhibition retained. Use of a tetrazole ring or 1,2,5-thiadiazolidine-3-one-1,1-dioxide as a carboxylate mimetic led to the discovery of two unique starting series that showed improved permeability (PAMPA) and potency of the order of 300nM. The SAR from these efforts underscores some of the major challenges in developing small molecule inhibitors for PTP1B.
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Affiliation(s)
- Zhao-Kui Wan
- Chemical and Screening Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
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41
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Taha MO, Bustanji Y, Al-Bakri AG, Yousef AM, Zalloum WA, Al-Masri IM, Atallah N. Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening. J Mol Graph Model 2007; 25:870-84. [PMID: 17035054 DOI: 10.1016/j.jmgm.2006.08.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 08/19/2006] [Accepted: 08/23/2006] [Indexed: 10/24/2022]
Abstract
A pharmacophoric model was developed for human protein tyrosine phosphatase 1B (h-PTP 1B) inhibitors utilizing the HipHop-REFINE module of CATALYST software. Subsequently, genetic algorithm and multiple linear regression analysis were employed to select an optimal combination of physicochemical descriptors and pharmacophore hypothesis that yield consistent QSAR equation of good predictive potential (r = 0.87,F-statistic = 69.13,r(BS)2 = 0.76,r(LOO)2 = 0.68). The validity of the QSAR equation and the associated pharmacophoric hypothesis was experimentally established by the identification of five new h-PTP 1B inhibitors retrieved from the National Cancer Institute (NCI) database.
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Affiliation(s)
- Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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42
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Mustelin T. Protein tyrosine phosphatases in human disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 584:53-72. [PMID: 16802599 DOI: 10.1007/0-387-34132-3_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tomas Mustelin
- Inflammatory and Infectious Disease Center, and Program of Signal Transduction, Cancer Center, The Burnham Institute, La Jolla, CA 92037, USA
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Congreve M, Murray CW, Carr R, Rees DC. Chapter 28 Fragment-Based Lead Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY VOLUME 42 2007. [DOI: 10.1016/s0065-7743(07)42028-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Winum JY, Scozzafava A, Montero JL, Supuran CT. Therapeutic potential of sulfamides as enzyme inhibitors. Med Res Rev 2006; 26:767-92. [PMID: 16710859 DOI: 10.1002/med.20068] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sulfamide, a quite simple molecule incorporating the sulfonamide functionality, widely used by medicinal chemists for the design of a host of biologically active derivatives with pharmacological applications, may give rise to at least five types of derivatives, by substituting one to four hydrogen atoms present in it, which show specific biological activities. Recently, some of these compounds started to be exploited for the design of many types of therapeutic agents. Among the enzymes for which sulfamide-based inhibitors were designed, are the carbonic anhydrases (CAs), a large number of proteases belonging to the aspartic protease (HIV-1 protease, gamma-secretase), serine protease (elastase, chymase, tryptase, and thrombin among others), and metalloprotease (carboxypeptidase A (CPA) and matrix metalloproteinases (MMP)) families. Some steroid sulfatase (STS) and protein tyrosine phosphatase inhibitors belonging to the sulfamide class of derivatives have also been reported. In all these compounds, many of which show low nanomolar affinity for the target enzymes for which they have been designed, the free or substituted sulfamide moiety plays important roles for the binding of the inhibitor to the active site cavity, either by directly coordinating to a metal ion found in some metalloenzymes (CAs, CPA, STS), usually by means of one of the nitrogen atoms present in the sulfamide motif, or as in the case of the cyclic sulfamides acting as HIV protease inhibitors, interacting with the catalytically critical aspartic acid residues of the active site by means of an oxygen atom belonging to the HN-SO2-NH motif, which substitutes a catalytically essential water molecule. In other cases, the sulfamide moiety is important for inducing desired physico-chemical properties to the drug-like compounds incorporating it, such as enhanced water solubility, better bioavailability, etc., because of the intrinsic properties of this highly polarized moiety when attached to an organic scaffold. This interesting motif is thus of great value for the design of pharmacological agents with a lot of applications.
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Affiliation(s)
- Jean-Yves Winum
- Université Montpellier II, Laboratoire de Chimie Biomoléculaire, UMR 5032, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex, France.
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Yue EW, Wayland B, Douty B, Crawley ML, McLaughlin E, Takvorian A, Wasserman Z, Bower MJ, Wei M, Li Y, Ala PJ, Gonneville L, Wynn R, Burn TC, Liu PCC, Combs AP. Isothiazolidinone heterocycles as inhibitors of protein tyrosine phosphatases: Synthesis and structure–activity relationships of a peptide scaffold. Bioorg Med Chem 2006; 14:5833-49. [PMID: 16769216 DOI: 10.1016/j.bmc.2006.05.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 05/15/2006] [Indexed: 01/18/2023]
Abstract
The structure-based design and discovery of the isothiazolidinone (IZD) heterocycle as a mimic of phosphotyrosine (pTyr) has led to the identification of novel IZD-containing inhibitors of protein tyrosine phosphatase 1B (PTP1B). The structure-activity relationships (SARs) of peptidic IZD-containing inhibitors of PTP1B are described along with a novel synthesis of the aryl-IZD fragments via a Suzuki coupling. The SAR revealed the saturated IZD heterocycle (42) is the most potent heterocyclic pTyr mimetic compared to the unsaturated IZD (25), the thiadiazolidinone (TDZ) (38), and the regioisomeric unsaturated IZD (31). The X-ray crystal structures of 11c and 25 complexed with PTP1B were solved and revealed nearly identical binding interactions in the active site. Ab initio calculations effectively explain the strong binding of the (S)-IZD due to the preorganized binding of the IZD in its low energy conformation.
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Affiliation(s)
- Eddy W Yue
- Incyte Corporation, Discovery Chemistry, Experimental Station, Route 141, Henry Clay Road, Wilmington, DE 19880, USA.
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46
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Ala PJ, Gonneville L, Hillman MC, Becker-Pasha M, Wei M, Reid BG, Klabe R, Yue EW, Wayland B, Douty B, Polam P, Wasserman Z, Bower M, Combs AP, Burn TC, Hollis GF, Wynn R. Structural basis for inhibition of protein-tyrosine phosphatase 1B by isothiazolidinone heterocyclic phosphonate mimetics. J Biol Chem 2006; 281:32784-95. [PMID: 16916797 DOI: 10.1074/jbc.m606873200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe(182) of the flap, and the side chain of Arg(221). When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors.
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Affiliation(s)
- Paul J Ala
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA.
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Abstract
Protein tyrosine phosphatases (PTPs) play vital roles in numerous cellular processes and are implicated in a growing number of human diseases, ranging from cancer to cardiovascular, immunological, infectious, neurological and metabolic diseases. There are at least 107 genes in the human genome, collectively referred to as the human 'PTPome'. Here the authors review the involvement of PTPs in human disease, discuss their potential as drug targets, and current efforts to develop PTP inhibitors for the treatment of human disease. Finally, the authors present their view of the future for PTPs as drug targets.
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Affiliation(s)
- Lutz Tautz
- Infectious and Inflammatory Disease and Cancer Center, The Burnham Institute, La Jolla, CA 92037, USA
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48
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Cho SY, Baek JY, Han SS, Kang SK, Ha JD, Ahn JH, Lee JD, Kim KR, Cheon HG, Rhee SD, Yang SD, Yon GH, Pak CS, Choi JK. PTP-1B inhibitors: Cyclopenta[d][1,2]-oxazine derivatives. Bioorg Med Chem Lett 2006; 16:499-502. [PMID: 16289879 DOI: 10.1016/j.bmcl.2005.10.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 10/07/2005] [Accepted: 10/19/2005] [Indexed: 11/24/2022]
Abstract
A series of novel cyclopenta[d][1,2]-oxazine derivatives was prepared and evaluated for their inhibitory activity toward protein tyrosine phosphatase 1B (PTP-1B). Compound 6s was found to be an inhibitor of PTP-1B with nanomolar IC(50) value and high level of selectivity over other recombinant phosphatases.
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Affiliation(s)
- Sung Yun Cho
- Bio-Organic Science Division, Korea Research Institute of Chemical Technology, 100 Jang-dong, Yuseong-gu, Daejeon 305-600, Republic of Korea
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49
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Leach AR, Hann MM, Burrows JN, Griffen EJ. Fragment screening: an introduction. MOLECULAR BIOSYSTEMS 2006; 2:430-46. [PMID: 17153140 DOI: 10.1039/b610069b] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There are clearly many different philosophies associated with adapting fragment screening into mainstream Drug Discovery Lead Generation strategies. Scientists at Astex, for instance, focus entirely on strategies involving use of X-ray crystallography and NMR. However, AstraZeneca uses a number of different fragment screening strategies. One approach is to screen a 2000 compound fragment set (with close to "lead-like" complexity) at 100 microM in parallel with every HTS such that the data are obtained on the entire screening collection at 10 microM plus the extra samples at 100 microM; this provides valuable compound potency data in a concentration range that is usually unexplored. The fragments are then screen-specific "privileged structures" that can be searched for in the rest of the HTS output and other databases as well as having synthesis follow-up. A typical workflow for a fragment screen within AstraZeneca is shown below (Figure 24) and highlights the desirability (particularly when screening >100 microM) for NMR and X-ray information to validate weak hits and give information on how to optimise them. In this chapter, we have provided an introduction to the theoretical and practical issues associated with the use of fragment methods and lead-likeness. Fragment-based approaches are still in an early stage of development and are just one of many interrelated techniques that are now used to identify novel lead compounds for drug development. Fragment based screening has some advantages, but like every other drug hunting strategy will not be universally applicable. There are in particular some practical challenges associated with fragment screening that relate to the generally lower level of potency that such compounds initially possess. Considerable synthetic effort has to be applied for post-fragment screening to build the sort of potency that would be expected to be found from a traditional HTS. However, if there are no low-hanging fruit in a screening collection to be found by HTS then the use of fragment screening can help find novelty that may lead to a target not being discarded as intractable. As such, the approach offers some significant advantages by providing less complex molecules, which may have better potential for novel drug optimisation and by enabling new chemical space to be more effectively explored. Many literature examples that cover examples of fragment screening approaches are still at the "proof of concept" stage and although delivering inhibitors or ligands, may still prove to be unsuitable when further ADMET and toxicity profiling is done. The next few years should see a maturing of the area, and as our understanding of how the concepts can be best applied, there are likely to be many more examples of attractive, small molecule hits, leads and candidate drugs derived from the approaches described.
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Affiliation(s)
- Andrew R Leach
- GlaxoSmithKline Research and Development, Gunnels Wood Road, Stevenage, Herts, UK
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50
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Winum JY, Scozzafava A, Montero JL, Supuran CT. The sulfamide motif in the design of enzyme inhibitors. Expert Opin Ther Pat 2005; 16:27-47. [DOI: 10.1517/13543776.16.1.27] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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