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Devi B, Vasishta SS, Das B, Baidya ATK, Rampa RS, Mahapatra MK, Kumar R. Integrated use of ligand and structure-based virtual screening, molecular dynamics, free energy calculation and ADME prediction for the identification of potential PTP1B inhibitors. Mol Divers 2024; 28:649-669. [PMID: 36745307 DOI: 10.1007/s11030-023-10608-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are the group of enzymes that control both cellular activity and the dephosphorylation of tyrosine (Tyr)-phosphorylated proteins. Dysregulation of PTP1B has contributed to numerous diseases including Diabetes Mellitus, Alzheimer's disease, and obesity rendering PTP1B as a legitimate target for therapeutic applications. It is highly challenging to target this enzyme because of its highly conserved and positively charged active-site pocket motivating researchers to find novel lead compounds against it. The present work makes use of an integrated approach combining ligand-based and structure-based virtual screening to find hit compounds targeting PTP1B. Initially, pharmacophore modeling was performed to find common features like two hydrogen bond acceptors, an aromatic ring and one hydrogen bond donor from the potent PTP1B inhibitors. The dataset of compounds matching with the common pharmacophoric features was filtered to remove Pan-Assay Interference substructure and to match the Lipinski criteria. Then, compounds were further prioritized using molecular docking and top fifty compounds with good binding affinity were selected for absorption, distribution, metabolism, and excretion (ADME) predictions. The top five compounds with high solubility, absorption and permeability holding score of - 10 to - 9.3 kcal/mol along with Ertiprotafib were submitted to all-atom molecular dynamic (MD) studies. The MD studies and binding free energy calculations showed that compound M4, M5 and M8 were having better binding affinity for PTP1B enzyme with ∆Gtotal score of - 24.25, - 31.47 and - 33.81 kcal/mol respectively than other compounds indicating that compound M8 could be a suitable lead compound as PTP1B inhibitor.
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Affiliation(s)
- Bharti Devi
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Sumukh Satyanarayana Vasishta
- Department of Chemical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Bhanuranjan Das
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Anurag T K Baidya
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Rahul Salmon Rampa
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | | | - Rajnish Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India.
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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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3
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Opekar S, Pohl R, Beran P, Rulíšek L, Beier P. Diethyl Fluoronitromethylphosphonate: Synthesis and Application in Nucleophilic Fluoroalkyl Additions. Chemistry 2013; 20:1453-8. [DOI: 10.1002/chem.201303817] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Indexed: 11/11/2022]
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4
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Opekar S, Pohl R, Eigner V, Beier P. Conjugate Addition of Diethyl 1-Fluoro-1-phenylsulfonylmethanephosphonate to α,β-Unsaturated Compounds. J Org Chem 2013; 78:4573-9. [DOI: 10.1021/jo400297f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stanislav Opekar
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Václav Eigner
- Department of Solid State Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague, Czech Republic
| | - Petr Beier
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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5
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Fu JP, He YH, Zhong J, Yang Y, Deng X, Guan Z. An efficient and general route to the synthesis of diethyl α,α-bromofluorophosphonates. J Fluor Chem 2011. [DOI: 10.1016/j.jfluchem.2011.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Guan Z, Wu D, Fu JP, He YH. A facile and efficient synthesis of diethyl α,α-chlorofluoroalkanephosphonates. HETEROATOM CHEMISTRY 2010. [DOI: 10.1002/hc.20604] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Romanenko VD, Kukhar VP. Fluorinated phosphonates: synthesis and biomedical application. Chem Rev 2007; 106:3868-935. [PMID: 16967924 DOI: 10.1021/cr051000q] [Citation(s) in RCA: 289] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vadim D Romanenko
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of the Ukraine, 1 Murmanska Street, Kyiv-94 02660, Ukraine
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8
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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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9
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Montalibet J, Skorey K, McKay D, Scapin G, Asante-Appiah E, Kennedy BP. Residues distant from the active site influence protein-tyrosine phosphatase 1B inhibitor binding. J Biol Chem 2005; 281:5258-66. [PMID: 16332678 DOI: 10.1074/jbc.m511546200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Regions of protein-tyrosine phosphatase (PTP) 1B that are distant from the active site yet affect inhibitor binding were identified by a novel library screen. This screen was based on the observation that expression of v-Src in yeast leads to lethality, which can be rescued by the coexpression of PTP1B. However, this rescue is lost when yeast are grown in the presence of PTP1B inhibitors. To identify regions of PTP1B (amino acids 1-400, catalytic domain plus 80-amino acid C-terminal tail) that can affect the binding of the difluoromethyl phosphonate (DFMP) inhibitor 7-bromo-6-difluoromethylphosphonate 3-naphthalenenitrile, a library coexpressing PTP1B mutants and v-Src was generated, and the ability of yeast to grow in the presence of the inhibitor was evaluated. PTP1B inhibitor-resistant mutations were found to concentrate on helix alpha7 and its surrounding region, but not in the active site. No resistant amino acid substitutions were found to occur in the C-terminal tail, suggesting that this region has little effect on active-site inhibitor binding. An in-depth characterization of a resistant substitution localizing to region alpha7 (S295F) revealed that this change minimally affected enzyme catalytic activity, but significantly reduced the potency of a panel of structurally diverse DFMP PTP1B inhibitors. This loss of inhibitor potency was found to be due to the difluoro moiety of these inhibitors because only the difluoro inhibitors were shifted. For example, the inhibitor potency of a monofluorinated or non-fluorinated analog of one of these DFMP inhibitors was only minimally affected. Using this type of library screen, which can scan the nearly full-length PTP1B sequence (catalytic domain and C-terminal tail) for effects on inhibitor binding, we have been able to identify novel regions of PTP1B that specifically affect the binding of DFMP inhibitors.
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Affiliation(s)
- Jacqueline Montalibet
- Department of Biochemistry and Molecular Biology, Merck Frosst Center for Therapeutic Research, Pointe-Claire, Quebec H9R 4P8, Canada
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10
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Blackburn GM, Türkmen H. Synthesis of α-fluoro- and α,α-difluoro-benzenemethanesulfonamides: new inhibitors of carbonic anhydrase. Org Biomol Chem 2005; 3:225-6. [PMID: 15632963 DOI: 10.1039/b417327a] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct fluorination of arenemethanesulfonamide anions under mild conditions and in high yield has been accomplished using N-fluorobisbenzenesulfonimide, NFSi, on carbanions of N-tert-butyl- and N-bis-(4-methoxyphenyl-methyl)-benzenemethanesulfonamides giving novel alpha-fluoro- and alpha,alpha-difluoro-benzenemethanesulfonamides respectively: IC(50) and pK(a) data show that alpha-halogenation enhances sulfonamide acidity incrementally and correlates well with increased carbonic anhydrase inhibition, while lipophilicity is also enhanced.
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Affiliation(s)
- G Michael Blackburn
- University of Sheffield, Department of Chemistry, Sheffield, S3 7HF, England.
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11
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Wang J, Chan SL, Ramnarayan K. Structure-based prediction of free energy changes of binding of PTP1B inhibitors. J Comput Aided Mol Des 2004; 17:495-513. [PMID: 14703121 DOI: 10.1023/b:jcam.0000004602.70594.5f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.
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Affiliation(s)
- Jing Wang
- Structural Bioinformatics Inc., 10929 Technology Place, San Diego, CA 92127, USA.
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12
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Dufresne C, Roy P, Wang Z, Asante-Appiah E, Cromlish W, Boie Y, Forghani F, Desmarais S, Wang Q, Skorey K, Waddleton D, Ramachandran C, Kennedy BP, Xu L, Gordon R, Chan CC, Leblanc Y. The development of potent non-peptidic PTP-1B inhibitors. Bioorg Med Chem Lett 2004; 14:1039-42. [PMID: 15013019 DOI: 10.1016/j.bmcl.2003.11.048] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Accepted: 11/14/2003] [Indexed: 11/18/2022]
Abstract
The SAR from our peptide libraries was exploited to design a series of potent deoxybenzoin PTP-1B inhibitors. The introduction of an ortho bromo substituent next to the difluoromethylphosphonate warhead gave up to 20-fold increase in potency compared to the desbromo analogues. In addition, these compounds were orally bioavailable and active in the animal models of non-insulin dependent diabetes mellitus (NIDDM).
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Affiliation(s)
- Claude Dufresne
- Department of Medicinal Chemistry, Merck Frosst Centre for Therapeutic Research, PO Box 1005, Pointe-Claire, Dorval, Canada H9R 4P8.
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13
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Hum G, Lee J, Taylor SD. Synthesis of [difluoro-(3-alkenylphenyl)-methyl]-phosphonic acids on non-crosslinked polystyrene and their evaluation as inhibitors of PTP1B. Bioorg Med Chem Lett 2002; 12:3471-4. [PMID: 12419386 DOI: 10.1016/s0960-894x(02)00768-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of [difluoro-(3-alkenylphenyl)-methyl]-phosphonates were prepared on non-crosslinked polystyrene, a soluble polymer support. After cleavage from the support, the resulting phosphonic acids were examined for inhibition with protein tyrosine phosphatase 1B. Compound 20, bearing an alpha,beta-unsaturated allyl ester moiety, was the most potent of this series of compounds, being a reversible, competitive inhibitor with a K(i) of 8.0+/-1.4 microM.
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Affiliation(s)
- Gabriel Hum
- Department of Chemistry, University of Waterloo, Ontario, Canada
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14
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Wang Q, Scheigetz J, Roy B, Ramachandran C, Gresser MJ. Novel caged fluorescein diphosphates as photoactivatable substrates for protein tyrosine phosphatases. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1601:19-28. [PMID: 12429499 DOI: 10.1016/s1570-9639(02)00412-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have characterized some novel caged fluorescein diphosphates as photoactivatable, cell-permeable substrates for protein tyrosine phosphatases and explored their usefulness in identifying inhibitors of tyrosine phosphatases. 1-(2-Nitrophenyl)ethyl protected fluorescein diphosphate (NPE-FDP) undergoes rapid photolysis to release FDP upon irradiation with a 450-W UV immersion lamp and its by-product does not inactivate protein tyrosine phosphatase 1B (PTP1B) or alters the viability of cells. The generated FDP from photolysis of NPE-FDP was shown to have exactly the same properties as FDP, which can be used as a PTP substrate in pure enzyme assays. We have also demonstrated that the PTP activity can be measured using NPE-FDP in small droplets. Its advantage as an inert substrate before photolysis allows the possibility of applying nanospray technology in screening and optimizing PTP inhibitors through a large chemical library. Like other caged bioeffectors such as nucleotide and inositol trisphosphate, NPE-FDP is cell-permeable. The NPE-FDP can be photolyzed to generate FDP inside cells, and then can be hydrolyzed by phosphatases to produce fluorescein monophosphate and subsequently to fluorescein. Although Jurkat cells contain high concentrations of CD45, it has not been possible to use FDP as a substrate to measure CD45 activity in the intact cell. This is due to the hydrolysis of FDP by several other cellular phosphatases. However, NPE-FDP can be useful as a cell-permeable substrate for overexpressed phosphatases such as alkaline phosphatase.
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Affiliation(s)
- Qingping Wang
- Department of Biochemistry and Molecular Biology, Merck Frosst Center for Therapeutic Research, P.O. Box 1005, Pointe-Claire, Dorval, Quebec, Canada H9R 4P8.
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15
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Ahn JH, Cho SY, Ha JD, Chu SY, Jung SH, Jung YS, Baek JY, Choi IK, Shin EY, Kang SK, Kim SS, Cheon HG, Yang SD, Choi JK. Synthesis and PTP1B inhibition of 1,2-naphthoquinone derivatives as potent anti-diabetic agents. Bioorg Med Chem Lett 2002; 12:1941-6. [PMID: 12113814 DOI: 10.1016/s0960-894x(02)00331-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A new series of 1,2-naphthoquinone derivatives was synthesized by various synthetic methods and evaluated for their ability to inhibit protein tyrosine phosphatase 1B (PTP1B). 1,2-Naphthoquinone derivatives with substituent at R(4) position showed submicromolar inhibitory activity, and compound 24 demonstrated 10- to 60-fold selectivity against the tested phosphatases. Also, several 4-aryl-1,2-naphthoquinone derivatives with substituents at R(3), R(6), R(7), or/and R(8) showed submicromolar inhibitory activity and good plasma stability.
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Affiliation(s)
- Jin Hee Ahn
- Medicinal Science Division, Korea Research Institute of Chemical Technology, Taejon 305-600, Republic of Korea
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16
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Leung C, Grzyb J, Lee J, Meyer N, Hum G, Jia C, Liu S, Taylor SD. The difluoromethylenesulfonic acid group as a monoanionic phosphate surrogate for obtaining PTP1B inhibitors. Bioorg Med Chem 2002; 10:2309-23. [PMID: 11983529 DOI: 10.1016/s0968-0896(02)00062-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Three peptides, 7-9, bearing sulfono(difluoromethyl)phenylalanine (F(2)Smp, 2), a nonhydrolyzable, monoanionic phosphotyrosine mimetic, were prepared and evaluated as PTP1B inhibitors. The most effective inhibitor was the nonapeptide, ELEF(F(2)Smp)MDYE-NH(2), (9) which exhibited a K(i) of 360 nM. A comparison of F(2)Smp-bearing peptides 7 [DADE(F(2)Smp)LNH(2), K(i)=3.4 microM] and 8 [EEDE(F(2)Smp)LNH(2), K(i)=0.74 microM] with their phosphono(difluoromethyl)phenylalanine (F(2)Pmp)-bearing analogues indicated that F(2)Smp is not as effective a pTyr mimetic as F(2)Pmp by 100- to 130-fold. Although F(2)Smp is not as effective as F(2)Pmp, a comparison of peptide 7 with analagous peptides bearing other monoanionic pTyr mimetics recently reported in the literature indicates that F(2)Smp is about 65-fold more effective than any other non-hydrolyzable, monanionic pTyr mimetic reported to date. To further assess the difluoromethylenesulfonic acid (DFMS) group as a monoanionic phosphate mimetic, a series of 24 nonpeptidyl biaryl compounds bearing the DFMS group were prepared using polymer-supported methodologies and screened for PTP1B inhibition. Several of these compounds were selected for further study and their IC(50)'s compared to their difluoromethylenephosphonic (DFMP) analogues. The differences in IC(50)'s between the DFMS and DFMP non-peptidyl compounds was not as great as with the F(2)Smp- and F(2)Pmp-bearing peptides. Possible reasons for this and its implication to the design of small molecule PTP1B inhibitors is discussed.
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Affiliation(s)
- Carmen Leung
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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17
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Abstract
A role for protein tyrosine phosphatases in the negative regulation of insulin signaling and a putative involvement in the insulin resistance associated with type 2 diabetes have been postulated since their discovery. The recent demonstration that mice lacking the protein tyrosine phosphatase-1B (PTP-1B) have enhanced insulin sensitivity validates this. Furthermore, when fed a high fat diet, these mice maintained insulin sensitivity and were resistant to obesity, suggesting that inhibition of PTP-1B activity could be a novel way of treating type 2 diabetes and obesity. This commentary reviews our current knowledge of PTP-1B in insulin signaling and its role in diabetes and discusses the development of potent and selective PTP-1B inhibitors.
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Affiliation(s)
- B P Kennedy
- Department of Biochemistry and Molecular Biology, Merck Frosst Center for Therapeutic Research, Pointe Claire-Dorval, H9R 4P8, Quebec, Canada.
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18
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Watanabe T, Suzuki T, Umezawa Y, Takeuchi T, Otsuka M, Umezawa K. Structure–Activity Relationship and Rational Design of 3,4-Dephostatin Derivatives as Protein Tyrosine Phosphatase Inhibitors. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(99)01058-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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20
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Wang Q, Scheigetz J, Gilbert M, Snider J, Ramachandran C. Fluorescein monophosphates as fluorogenic substrates for protein tyrosine phosphatases. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1431:14-23. [PMID: 10209274 DOI: 10.1016/s0167-4838(99)00042-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A series of novel fluorescein monophosphates aimed as substrates for protein tyrosine phosphatases (PTPs) were synthesized and evaluated against fluorescein diphosphate (FDP), the currently used fluorescent substrate for PTPs. In contrast to FDP, which is dephosphorylated to monophosphate and then to fluorescein in a sequential reaction, these monophosphates are dephosphorylated in a single step. This eliminates the complication in assaying PTPs due to the cleavage of the second phosphate group. The kinetic studies of these substrates with PTPs were performed and Michaelis-Menten parameters were obtained. These designed substrates have Km 0.03-0. 35 mM, kcat/Km of 3-100 mM-1 s-1 with CD45 and PTP1B. The results showed that the substrates with negative charge groups on the fluorescein have higher affinities for PTP1B, which are consistent with other observations. In this series, fluorescein monosulfate monophosphate (FMSP) was the best substrate observed. Since FMSP showed large increases in both absorption and fluorescence upon dephosphorylation by PTPs at pH>6.0, it is one of the most sensitive, stable and high affinity substrates reported for PTPs.
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Affiliation(s)
- Q Wang
- Department of Biochemistry and Molecular Biology, Merck-Frosst Center for Therapeutic Research, P.O. Box 1005, Pointe-Claire-Dorval, Que. H9R 4P8, Canada.
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21
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22
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Yokomatsu T, Murano T, Umesue I, Soeda S, Shimeno H, Shibuya S. Synthesis and biological evaluation of alpha,alpha-difluorobenzylphosphonic acid derivatives as small molecular inhibitors of protein-tyrosine phosphatase 1B. Bioorg Med Chem Lett 1999; 9:529-32. [PMID: 10098656 DOI: 10.1016/s0960-894x(99)00027-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A series of alpha,alpha-difluorobenzylphosphonic acids having a hydrophobic functional group were prepared via the Stille coupling reaction from halogenated alpha,alpha-difluorobenzylphosphonates. Evaluation of inhibitory activity toward protein tyrosine phosphatase (PTP 1B) revealed that the ethynyl, phenylethynyl and (E)-styryl groups on the benzene nuclei increased the inhibitory activity of alpha,alpha-difluorobenzylphosphonic acid. Inhibitory activities significantly increased upon introducing both (E)-styryl and bis-methylsulfonamide functional groups onto the benzene nuclei of alpha,alpha-difluorobenzylphosphonic acid.
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Affiliation(s)
- T Yokomatsu
- School of Pharmacy, Tokyo University of Pharmacy & Life Science, Horinouchi, Hachioji, Japan
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23
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Kotoris CC, Chen MJ, Taylor SD. Novel phosphate mimetics for the design of non-peptidyl inhibitors of protein tyrosine phosphatases. Bioorg Med Chem Lett 1998; 8:3275-80. [PMID: 9873717 DOI: 10.1016/s0960-894x(98)00598-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Benzylic alpha,alpha-difluorosulfonates, alpha,alpha-difluorotetrazoles, and alpha,alpha-difluorocarboxylates of type 5 and 6 were synthesized and examined as potential phosphate biosteres for PTP1B inhibition. The alpha,alpha-difluorosulfonates and alpha,alpha-difluorotetrazoles were found to be more effective inhibitors than the analogous compounds bearing the fluoromalonyl group, a phosphate biostere currently being used for PTP inhibition.
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Affiliation(s)
- C C Kotoris
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
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Kotoris CC, Chen MJ, Taylor SD. Preparation of Benzylic α,α-Difluoronitriles, -tetrazoles, and -sulfonates via Electrophilic Fluorination. J Org Chem 1998. [DOI: 10.1021/jo981163x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher C. Kotoris
- Department of Chemistry, University of Toronto, Mississauga Campus, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Mei-Jin Chen
- Department of Chemistry, University of Toronto, Mississauga Campus, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Scott D. Taylor
- Department of Chemistry, University of Toronto, Mississauga Campus, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6
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Yao ZJ, Ye B, Wu XW, Wang S, Wu L, Zhang ZY, Burke TR. Structure-based design and synthesis of small molecule protein-tyrosine phosphatase 1B inhibitors. Bioorg Med Chem 1998; 6:1799-810. [PMID: 9839010 DOI: 10.1016/s0968-0896(98)00140-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein-tyrosine phosphatase (PTP) inhibitors are attractive as potential signal transduction-directed therapeutics which may be useful in the treatment of a variety of diseases. We have previously reported the X-ray structure of 1,1-difluoro-1-(2-naphthalenyl)methyl] phosphonic acid (4) complexed with the human the protein-tyrosine phosphatase 1B (PTP1B) and its use in the design of an analogue which binds with higher affinity within the catalytic site (Burke, T. R., Jr. et al. Biochemistry 1996, 35, 15989). In the current study, new naphthyldifluoromethyl phosphonic acids were designed bearing acidic functionality intended to interact with the PTP1B Arg47, which is situated just outside the catalytic pocket. This residue has been shown previously to provide key interactions with acidic residues of phosphotyrosyl-containing peptide substrates. Consistent with trends predicted by molecular dynamics calculations, the new analogues bound with 7- to 14-fold higher affinity than the parent 4, in principal validating the design rationale.
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Affiliation(s)
- Z J Yao
- Laboratory of Medicinal Chemistry, National Institutes of Health, Bethesda, MD 20892, USA
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Li Z, Yeo SL, Pallen CJ, Ganesan A. Solid-phase synthesis of potential protein tyrosine phosphatase inhibitors via the Ugi four-component condensation. Bioorg Med Chem Lett 1998; 8:2443-6. [PMID: 9873558 DOI: 10.1016/s0960-894x(98)00408-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A library of 108 alpha,alpha-difluoromethylenephosphonic acids was prepared by Ugi four-component condensation using Rink-NH2 resin, 4-[(diethoxyphosphinyl) difluoromethyl]benzoic acid, and a set of 18 aldehydes and 6 isonitriles. Following resin cleavage, the diethylphosphonate esters were hydrolyzed with trimethylsilyl bromide to yield the free acids which were assayed for inhibition of PTP alpha, PTP beta and PTP epsilon.
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Affiliation(s)
- Z Li
- Institute of Molecular and Cell Biology, National University of Singapore
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Taylor SD, Kotoris CC, Dinaut AN, Wang Q, Ramachandran C, Huang Z. Potent non-peptidyl inhibitors of protein tyrosine phosphatase 1B. Bioorg Med Chem 1998; 6:1457-68. [PMID: 9801817 DOI: 10.1016/s0968-0896(98)00075-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The development of inhibitors of protein tyrosine phosphatases (PTPs) has recently been the subject of intensive investigation due to their potential as chemotherapeutics and as tools for studying signal transduction pathways. Here we report the evaluation of a variety of small molecule, non-peptidyl inhibitors of protein tyrosine phosphatase 1B (PTP1B), bearing the alpha, alpha-difluoromethylenephosphonic acid (DFMP) group, a non-hydrolyzable phosphate mimetic. A series of phenyl derivatives bearing a single DFMP group were initially surveyed. In general, these were not significantly more potent inhibitors than the parent compound, alpha, alpha-difluorobenzylphosphonic acid, with the exception being the meta-phenyl substituted species which decreased the IC50 by approximately 17-fold relative to alpha, alpha-difluorobenzylphosphonic acid. However, certain compounds bearing two DFMP moieties were very potent inhibitors. Some of these are among the most potent small molecule inhibitors of any PTP reported to date with the best one exhibiting a Ki of 1.5 microM. The structural basis for these results are discussed. One of the bis-DFMP inhibitors was examined in detail and it was found that the fluorines were essential for potent inhibition. Inhibition was independent of pH between pH 5.5-7.2 suggesting that both the mono and dianionic forms of the individual DFMP groups bind equally well. The trends observed in the inhibitory potency of these compounds with PTP1B were very similar to the trends observed by other workers on the K(m)'s of the analogous phenylphosphate substrates with rat PTP1. This indicates that studies of non-peptidyl substrates with rat PTP1 can be used as a guide for the development of human PTP1B inhibitors.
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Affiliation(s)
- S D Taylor
- Department of Chemistry, Erindale College, University of Toronto, Mississauga, Ontario, Canada.
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