1
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Woods VA, Abzalimov RR, Keedy DA. Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS. Protein Sci 2024; 33:e5024. [PMID: 38801229 PMCID: PMC11129624 DOI: 10.1002/pro.5024] [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: 11/14/2023] [Revised: 03/27/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for obesity, diabetes, and certain types of cancer. In particular, allosteric inhibitors hold potential for therapeutic use, but an incomplete understanding of conformational dynamics and allostery in this protein has hindered their development. Here, we interrogate solution dynamics and allosteric responses in PTP1B using high-resolution hydrogen-deuterium exchange mass spectrometry (HDX-MS), an emerging and powerful biophysical technique. Using HDX-MS, we obtain a detailed map of backbone amide exchange that serves as a proxy for the solution dynamics of apo PTP1B, revealing several flexible loops interspersed among more constrained and rigid regions within the protein structure, as well as local regions that exchange faster than expected from their secondary structure and solvent accessibility. We demonstrate that our HDX rate data obtained in solution adds value to estimates of conformational heterogeneity derived from a pseudo-ensemble constructed from ~200 crystal structures of PTP1B. Furthermore, we report HDX-MS maps for PTP1B with active-site versus allosteric small-molecule inhibitors. These maps suggest distinct and widespread effects on protein dynamics relative to the apo form, including changes in locations distal (>35 Å) from the respective ligand binding sites. These results illuminate that allosteric inhibitors of PTP1B can induce unexpected changes in dynamics that extend beyond the previously understood allosteric network. Together, our data suggest a model of BB3 allostery in PTP1B that combines conformational restriction of active-site residues with compensatory liberation of distal residues that aid in entropic balancing. Overall, our work showcases the potential of HDX-MS for elucidating aspects of protein conformational dynamics and allosteric effects of small-molecule ligands and highlights the potential of integrating HDX-MS alongside other complementary methods, such as room-temperature X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations, to guide the development of new therapeutics.
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Affiliation(s)
- Virgil A. Woods
- Structural Biology InitiativeCUNY Advanced Science Research CenterNew YorkNew YorkUSA
- PhD Program in BiochemistryCUNY Graduate CenterNew YorkNew YorkUSA
| | - Rinat R. Abzalimov
- Structural Biology InitiativeCUNY Advanced Science Research CenterNew YorkNew YorkUSA
| | - Daniel A. Keedy
- Structural Biology InitiativeCUNY Advanced Science Research CenterNew YorkNew YorkUSA
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkNew YorkUSA
- PhD Programs in Biochemistry, Biology, & ChemistryCUNY Graduate CenterNew YorkNew YorkUSA
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2
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Rezhdo A, Hershman RL, Van Deventer JA. Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596443. [PMID: 38853888 PMCID: PMC11160716 DOI: 10.1101/2024.05.29.596443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In vitro display technologies, exemplified by phage and yeast display, have emerged as powerful platforms for antibody discovery and engineering. However, the identification of antibodies that disrupt target functions beyond binding remains a challenge. In particular, there are very few strategies that support identification and engineering of either protein-based irreversible binders or inhibitory enzyme binders. Expanding the range of chemistries in antibody libraries has the potential to lead to efficient discovery of function-disrupting antibodies. In this work, we describe a yeast display-based platform for the discovery of chemically diversified antibodies. We constructed a billion-member antibody library that supports the presentation of a range of chemistries within antibody variable domains via noncanonical amino acid (ncAA) incorporation and subsequent bioorthogonal click chemistry conjugations. Use of a polyspecific orthogonal translation system enables introduction of chemical groups with various properties, including photo-reactive, proximity-reactive, and click chemistry-enabled functional groups for library screening. We established conjugation conditions that facilitate modification of the full library, demonstrating the feasibility of sorting the full billion-member library in "protein-small molecule hybrid" format in future work. Here, we conducted initial library screens after introducing O-(2-bromoethyl)tyrosine (OBeY), a weakly electrophilic ncAA capable of undergoing proximity-induced crosslinking to a target. Enrichments against donkey IgG and protein tyrosine phosphatase 1B (PTP1B) each led to the identification of several OBeY-substituted clones that bind to the targets of interest. Flow cytometry analysis on the yeast surface confirmed higher retention of binding for OBeY-substituted clones compared to clones substituted with ncAAs lacking electrophilic side chains after denaturation. However, subsequent crosslinking experiments in solution with ncAA-substituted clones yielded inconclusive results, suggesting that weakly reactive OBeY side chain is not sufficient to drive robust crosslinking in the clones isolated here. Nonetheless, this work establishes a multi-modal, chemically expanded antibody library and demonstrates the feasibility of conducting discovery campaigns in chemically expanded format. This versatile platform offers new opportunities for identifying and characterizing antibodies with properties beyond what is accessible with the canonical amino acids, potentially enabling discovery of new classes of reagents, diagnostics, and even therapeutic leads.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Rebecca L Hershman
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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3
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Aguilar-Ramírez E, Reyes-Pérez V, Fajardo-Hernández CA, Quezada-Suaste CD, Carreón-Escalante M, Merlin-Lucas V, Quiroz-García B, Granados-Soto V, Rivera-Chávez J. Harnessing the Reactivity of Duclauxin toward Obtaining hPTP1B 1-400 Inhibitors. J Med Chem 2023; 66:16222-16234. [PMID: 38051546 DOI: 10.1021/acs.jmedchem.3c01594] [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: 12/07/2023]
Abstract
Duclauxin (1) from Talaromyces sp. IQ-313 was reported as a putative allosteric modulator of human recombinant protein tyrosine phosphatase 1B (400 amino acids) (hPTP1B1-400), a validated target for the treatment of type II diabetes. Based on these findings, a one-strain-many-compound (OSMAC) experiment on the IQ-313 strain generated derivatives 5a, 6, and 7. Moreover, a one-/two-step semisynthetic approach guided by docking toward hPTP1B1-400 produced 38 analogs, a series (A) incorporating a lactam functionalization at C-1 (8a-15a, 36a, and 37a) and a series (B) containing a lactam at C-1 and an extra unsaturation between C-7 and C-8 (5b, 11b-37b). In vitro evaluation and structure-activity relationship (SAR) analysis revealed that analogs from the B series are up to 10-fold more active than 1 and derivatives from the A series. Furthermore, duclauxin (1) and 36b were assessed for their potential acute toxicity, estimating their LD50 to be higher than 300 mg/kg. Moreover, 36b significantly reduced glycemia in an insulin tolerance test in mice, suggesting that its mechanism of action is through the PTP1B inhibition.
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Affiliation(s)
- Enrique Aguilar-Ramírez
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Valeria Reyes-Pérez
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Carlos A Fajardo-Hernández
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Carlos D Quezada-Suaste
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mario Carreón-Escalante
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Verenice Merlin-Lucas
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Beatriz Quiroz-García
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Vinicio Granados-Soto
- Pharmacobiology Department, Centro de Investigación y de Estudios Avanzados, Sede Sur, Mexico City 14330, Mexico
| | - José Rivera-Chávez
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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4
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Woods VA, Abzalimov RR, Keedy DA. Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548582. [PMID: 37503000 PMCID: PMC10369962 DOI: 10.1101/2023.07.12.548582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for obesity, diabetes, and certain types of cancer. In particular, allosteric inhibitors hold potential for therapeutic use, but an incomplete understanding of conformational dynamics and allostery in this protein has hindered their development. Here, we interrogate solution dynamics and allosteric responses in PTP1B using high-resolution hydrogen-deuterium exchange mass spectrometry (HDX-MS), an emerging and powerful biophysical technique. Using HDX-MS, we obtain a detailed map of the solution dynamics of apo PTP1B, revealing several flexible loops interspersed among more constrained and rigid regions within the protein structure, as well as local regions that exchange faster than expected from their secondary structure and buriedness. We demonstrate that our HDX rate data obtained in solution adds value to predictions of dynamics derived from a pseudo-ensemble constructed from ~200 crystal structures of PTP1B. Furthermore, we report HDX-MS maps for PTP1B with active-site vs. allosteric small-molecule inhibitors. These maps reveal distinct, dramatic, and widespread effects on protein dynamics relative to the apo form, including changes to dynamics in locations distal (>35 Å) from the respective ligand binding sites. These results help shed light on the allosteric nature of PTP1B and the surprisingly far-reaching consequences of inhibitor binding in this important protein. Overall, our work showcases the potential of HDX-MS for elucidating protein conformational dynamics and allosteric effects of small-molecule ligands, and highlights the potential of integrating HDX-MS alongside other complementary methods to guide the development of new therapeutics.
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Affiliation(s)
- Virgil A. Woods
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Rinat R. Abzalimov
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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5
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Hong SH, Xi SY, Johns AC, Tang LC, Li A, Hum MN, Chartier CA, Jovanovic M, Shah NH. Mapping the Chemical Space of Active-Site Targeted Covalent Ligands for Protein Tyrosine Phosphatases. Chembiochem 2023; 24:e202200706. [PMID: 36893077 PMCID: PMC10192133 DOI: 10.1002/cbic.202200706] [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: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/10/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their biological roles or as leads for the development of new therapeutics. In this study, we explore an array of electrophiles and fragment scaffolds to investigate the required chemical parameters for covalent inhibition of tyrosine phosphatases. Our analysis juxtaposes the intrinsic electrophilicity of these compounds with their potency against several classical PTPs, revealing chemotypes that inhibit tyrosine phosphatases while minimizing excessive, potentially non-specific reactivity. We also assess sequence divergence at key residues in PTPs to explain their differential susceptibility to covalent inhibition. We anticipate that our study will inspire new strategies to develop covalent probes and inhibitors for tyrosine phosphatases.
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Affiliation(s)
- Suk ho Hong
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Sarah Y. Xi
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Andrew C. Johns
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Madeleine N. Hum
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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6
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Zhu Z, Tang R, Huff S, Kummetha IR, Wang L, Li N, Rana TM. Small-molecule PTPN2 Inhibitors Sensitize Resistant Melanoma to Anti-PD-1 Immunotherapy. CANCER RESEARCH COMMUNICATIONS 2023; 3:119-129. [PMID: 36968224 PMCID: PMC10035454 DOI: 10.1158/2767-9764.crc-21-0186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 08/23/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Although immune checkpoint inhibitors targeting T-cell immunoregulatory proteins have revolutionized cancer treatment, they are effective only in a limited number of patients, and new strategies are needed to enhance tumor responses to immunotherapies. Deletion of protein tyrosine phosphatase non-receptor type 2 (Ptpn2), a regulator of growth factor and cytokine signaling pathways, has been shown to sensitize murine B16F10 melanoma cells to IFNγ and anti-PD-1 immunotherapy. Here, we investigated the potential therapeutic utility of small-molecule PTPN2 inhibitors. Ten inhibitors were synthesized on the basis of in silico modeling and structure-based design and functionally tested in vitro and in vivo. We show that the inhibitors had little effect on B16F10 cells alone, but effectively sensitized the tumor cells to IFNγ treatment in vitro and to anti-PD-1 therapy in vivo. Under both conditions, Ptpn2 inhibitor cotreatment suppressed B16F10 cell growth and enhanced Stat1 phosphorylation and expression of IFNγ response genes. In vivo, PTPN2 inhibitor cotreatment significantly reduced melanoma and colorectal tumor growth and enhanced mouse survival compared with anti-PD-1 treatment alone, and this was accompanied by increased tumor infiltration by granzyme B+ CD8+ T cells. Similar results were obtained with representative murine and human colon cancer and lung cancer cell lines. Collectively, these results demonstrate that small-molecule inhibitors of PTPN2 may have clinical utility as sensitizing agents for immunotherapy-resistant cancers. Significance To enhance the effectiveness of immunotherapies in resistant or nonresponsive cancers, it is important to develop inhibitors of enzymes that negatively influence the outcome of treatments. We have designed and evaluated small-molecule inhibitors of PTPN2 demonstrating that these compounds may have clinical utility as sensitizing agents for immunotherapy-resistant cancers.
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Affiliation(s)
- Zhouting Zhu
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Rachel Tang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Sarah Huff
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Indrasena Reddy Kummetha
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Lingling Wang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Na Li
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Tariq M. Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, La Jolla, California
- San Diego Center for Precision Immunotherapy, Moores Cancer Center, University of California San Diego, La Jolla, California
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7
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Torgeson KR, Clarkson MW, Granata D, Lindorff-Larsen K, Page R, Peti W. Conserved conformational dynamics determine enzyme activity. SCIENCE ADVANCES 2022; 8:eabo5546. [PMID: 35921420 PMCID: PMC9348788 DOI: 10.1126/sciadv.abo5546] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.
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Affiliation(s)
- Kristiane R. Torgeson
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, USA
- Department of Cell Biology, University of Connecticut Health, Farmington, CT, USA
| | - Michael W. Clarkson
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, USA
| | - Daniele Granata
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health, Farmington, CT, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, USA
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8
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Greisman JB, Dalton KM, Sheehan CJ, Klureza MA, Kurinov I, Hekstra DR. Native SAD phasing at room temperature. Acta Crystallogr D Struct Biol 2022; 78:986-996. [PMID: 35916223 PMCID: PMC9344477 DOI: 10.1107/s2059798322006799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Single-wavelength anomalous diffraction (SAD) is a routine method for overcoming the phase problem when solving macromolecular structures. This technique requires the accurate measurement of intensities to determine differences between Bijvoet pairs. Although SAD experiments are commonly conducted at cryogenic temperatures to mitigate the effects of radiation damage, such temperatures can alter the conformational ensemble of the protein and may impede the merging of data from multiple crystals due to non-uniform freezing. Here, a strategy is presented to obtain high-quality data from room-temperature, single-crystal experiments. To illustrate the strengths of this approach, native SAD phasing at 6.55 keV was used to solve four structures of three model systems at 295 K. The resulting data sets allow automatic phasing and model building, and reveal alternate conformations that reflect the structure of proteins at room temperature.
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9
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Liu R, Mathieu C, Berthelet J, Zhang W, Dupret JM, Rodrigues Lima F. Human Protein Tyrosine Phosphatase 1B (PTP1B): From Structure to Clinical Inhibitor Perspectives. Int J Mol Sci 2022; 23:ijms23137027. [PMID: 35806030 PMCID: PMC9266911 DOI: 10.3390/ijms23137027] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation is an essential process in biological events and is considered critical for biological functions. In tissues, protein phosphorylation mainly occurs on tyrosine (Tyr), serine (Ser) and threonine (Thr) residues. The balance between phosphorylation and dephosphorylation is under the control of two super enzyme families, protein kinases (PKs) and protein phosphatases (PPs), respectively. Although there are many selective and effective drugs targeting phosphokinases, developing drugs targeting phosphatases is challenging. PTP1B, one of the most central protein tyrosine phosphatases (PTPs), is a key player in several human diseases and disorders, such as diabetes, obesity, and hematopoietic malignancies, through modulation of different signaling pathways. However, due to high conservation among PTPs, most PTP1B inhibitors lack specificity, raising the need to develop new strategies targeting this enzyme. In this mini-review, we summarize three classes of PTP1B inhibitors with different mechanisms: (1) targeting multiple aryl-phosphorylation sites including the catalytic site of PTP1B; (2) targeting allosteric sites of PTP1B; (3) targeting specific mRNA sequence of PTP1B. All three types of PTP1B inhibitors present good specificity over other PTPs and are promising for the development of efficient small molecules targeting this enzyme.
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Affiliation(s)
- Rongxing Liu
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
| | | | - Jérémy Berthelet
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
- Centre Epigénétique et Destin Cellulaire, Université Paris Cité, CNRS, F-75013 Paris, France
| | - Wenchao Zhang
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jean-Marie Dupret
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
| | - Fernando Rodrigues Lima
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
- Correspondence:
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10
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Recent Updates on Development of Protein-Tyrosine Phosphatase 1B Inhibitors for Treatment of Diabetes, Obesity and Related Disorders. Bioorg Chem 2022; 121:105626. [DOI: 10.1016/j.bioorg.2022.105626] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/19/2021] [Accepted: 01/13/2022] [Indexed: 01/30/2023]
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11
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Martínez-Aldino IY, Villaseca-Murillo M, Morales-Jiménez J, Rivera-Chávez J. Absolute configuration and protein tyrosine phosphatase 1B inhibitory activity of xanthoepocin, a dimeric naphtopyrone from Penicillium sp. IQ-429. Bioorg Chem 2021; 115:105166. [PMID: 34384957 DOI: 10.1016/j.bioorg.2021.105166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 12/19/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an active target for developing drugs to treat type II diabetes, obesity, and cancer. However, in the past, research programs targeting this enzyme focused on discovering inhibitors of truncated models (hPTP1B1-282, hPTP1B1-298, or hPTP1B1-321), losing valuable information about the ligands' mechanism of inhibition and selectivity. Nevertheless, finding an allosteric site in hPTP1B1-321, and the full-length (hPTP1B1-400) protein expression, have shifted the strategies to discover new PTP1B inhibitors. Accordingly, as part of a research program directed at finding non-competitive inhibitors of hPTP1B1-400 from Pezizomycotina, the extract of Penicillium sp. (IQ-429) was chemically investigated. This study led to xanthoepocin (1) isolation, which was elucidated by means of spectroscopic and spectrometric data. The absolute configuration of 1 was determined to be 7R8S9R7'R8'S9'R by comparing the theoretical and experimental ECD spectra and by GIAO-NMR DP4 + statistical analysis. Xanthoepocin (1) inhibited the phosphatase activity of hPTP1B1-400 (IC50 value of 8.8 ± 1.0 µM) in a mixed type fashion, with ki and αki values of 5.5 and 6.6 μM, respectively. Docking xanthoepocin (1) with a homologated model of hPTP1B1-400 indicated that it binds in a pocket different from the catalytic triad at the interface of the N and C-terminal domains. Molecular dynamics (MD) simulations showed that 1 locks the WPD loop of hPTP1B1-400 in a closed conformation, avoiding substrate binding, products release, and catalysis, suggesting an allosteric modulation triggered by large-scale conformational and dynamics changes. Intrinsic quenching fluorescence experiments indicated that 1 behaves like a static quencher of hPTP1B1-400 (KSV = 1.1 × 105 M-1), and corroborated that it binds to the enzyme with an affinity constant (ka) of 3.7 × 105 M-1. Finally, the drug-likeness and medicinal chemistry friendliness of 1 were predicted with SwissADME.
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Affiliation(s)
- Ingrid Y Martínez-Aldino
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria 04510, Ciudad de México, Mexico
| | - Martha Villaseca-Murillo
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria 04510, Ciudad de México, Mexico
| | - Jesús Morales-Jiménez
- CONACYT-Consorcio de Investigación, Innovación y Desarrollo para las Zonas Áridas (CIIDZA), Instituto Potosino de Investigación Científica y Tecnológica A. C., Camino a la Presa San José 2055, Lomas 4a sección, 78216 San Luis Potosí, Mexico.
| | - José Rivera-Chávez
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria 04510, Ciudad de México, Mexico.
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12
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Abbasi K, Razzaghi P, Poso A, Amanlou M, Ghasemi JB, Masoudi-Nejad A. DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks. Bioinformatics 2021; 36:4633-4642. [PMID: 32462178 DOI: 10.1093/bioinformatics/btaa544] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/29/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION An essential part of drug discovery is the accurate prediction of the binding affinity of new compound-protein pairs. Most of the standard computational methods assume that compounds or proteins of the test data are observed during the training phase. However, in real-world situations, the test and training data are sampled from different domains with different distributions. To cope with this challenge, we propose a deep learning-based approach that consists of three steps. In the first step, the training encoder network learns a novel representation of compounds and proteins. To this end, we combine convolutional layers and long-short-term memory layers so that the occurrence patterns of local substructures through a protein and a compound sequence are learned. Also, to encode the interaction strength of the protein and compound substructures, we propose a two-sided attention mechanism. In the second phase, to deal with the different distributions of the training and test domains, a feature encoder network is learned for the test domain by utilizing an adversarial domain adaptation approach. In the third phase, the learned test encoder network is applied to new compound-protein pairs to predict their binding affinity. RESULTS To evaluate the proposed approach, we applied it to KIBA, Davis and BindingDB datasets. The results show that the proposed method learns a more reliable model for the test domain in more challenging situations. AVAILABILITY AND IMPLEMENTATION https://github.com/LBBSoft/DeepCDA.
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Affiliation(s)
- Karim Abbasi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614411, Iran
| | - Parvin Razzaghi
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 4513766731, Iran
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 80100, Finland
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran 1416753955, Iran
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, University of Tehran, Tehran 1417614418, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614411, Iran
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13
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Sarkar P, Thirumurugan K. New insights into TNFα/PTP1B and PPARγ pathway through RNF213- a link between inflammation, obesity, insulin resistance, and Moyamoya disease. Gene 2020; 771:145340. [PMID: 33333224 DOI: 10.1016/j.gene.2020.145340] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 01/02/2023]
Abstract
Diabetic patients are always at a higher risk of ischemic diseases like coronary artery diseases. One such ischemic carotid artery disease is Moyamoya disease (MMD) associated with diabetes Type I and II, but the causality was unclear. Ring Finger Protein 213 (RNF213) is the major susceptible gene for MMD. To understand the association between diabetes mellitus and MMD we chose the major players from both of the anomalies: insulin and RNF213. But before establishing the role of RNF213 in the insulin-regulating pathway we had to understand the involvement of RNF213 within different biological systems. For this, we have adopted a preliminary computational approach to find the prominent interactions of RNF213. Our first objective was to construct an interactome for RNF213. We have analyzed several curated databases and adapted a list of RNF213 interacting partners to develop its interactome. Then to understand the involvement of this interactome in biological functions we have analyzed major biological pathways, biological processes, and prominent clusters related to this interactome through a computational approach. Then to develop a pathway that might give clues for RNF213 involvement in the insulin regulatory pathway we have validated the intercluster and intracluster predictions and identified a regulatory pathway for RNF213. RNF213 interactome was observed to be involved in adaptive immunity with 4 major clusters; one of the clusters involved TNFα. The immune system involves several pathways, and therefore at this point, we have chosen an event-based strategy to obtain an explicit target. Immunity is mediated by pro-inflammatory cytokines like TNFα. TNFα-mediated inflammation, obesity, and insulin resistance are associated. Therefore we chose to explore the role of RNF213 in TNFα-mediated inflammation in macrophages and inflammation-mediated insulin-resistance in adipocytes. We have observed an enhancement of RNF213 gene expression by LPS mediated pro-inflammatory stimuli and suppression by PPARγ-mediated anti-inflammatory, insulin-sensitizing stimuli in macrophages, and also in adipocytes. Administration of the pro-inflammatory cytokine TNFα was able to impede the reduction in RNF213 expression during adipogenesis and this effect was observed to be mediated by PTP1B. Inactivation of PTP1B abolished RNF213 expression which in turn enhanced the adipogenesis process through enhanced PPARγ. Constitutive expression of RNF213 suppressed the adipocyte differentiation by the inhibition of PPARγ. We could show the regulation of RNF213 by TNFα/PTP1B pathway and PPARγ. The constitutive expression of RNF213 during adipogenesis appears to be an adipostatic measure that obese patients acquire to inhibit further adipogenesis. This is verified in silico by analyzing the gene expression data obtained from the Gene Expression Omnibus database, which showed a higher expression of RNF213 in adipose tissue samples of obese people. Overall this study gives new insights into the TNFα-mediated pathway in adipogenesis and suggests the role of RNF213 in adipogenesis via this pathway.
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Affiliation(s)
- Priyanka Sarkar
- 206, Structural Biology Lab, Centre for Biomedical Research, School of Biosciences & Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Kavitha Thirumurugan
- 206, Structural Biology Lab, Centre for Biomedical Research, School of Biosciences & Technology, Vellore Institute of Technology, Vellore 632014, India.
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14
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Torgeson KR, Clarkson MW, Kumar GS, Page R, Peti W. Cooperative dynamics across distinct structural elements regulate PTP1B activity. J Biol Chem 2020; 295:13829-13837. [PMID: 32737198 DOI: 10.1074/jbc.ra120.014652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Protein-tyrosine phosphatase 1B (PTP1B) is the canonical enzyme for investigating how distinct structural elements influence enzyme catalytic activity. Although it is recognized that dynamics are essential for PTP1B function, the data collected thus far have not resolved whether distinct elements are dynamically coordinated or, alternatively, whether they fulfill their respective functions independently. To answer this question, we performed a comprehensive 13C-methyl relaxation study of Ile, Leu, and Val (ILV) residues of PTP1B, which, because of its substantially increased sensitivity, provides a comprehensive understanding of the influence of protein motions on different time scales for enzyme function. We discovered that PTP1B exhibits dynamics at three distinct time scales. First, it undergoes a distinctive slow motion that allows for the dynamic binding and release of its two most N-terminal helices from the catalytic core. Second, we showed that PTP1B 13C-methyl group side chain fast time-scale dynamics and 15N backbone fast time-scale dynamics are fully consistent, demonstrating that fast fluctuations are essential for the allosteric control of PTP1B activity. Third, and most importantly, using 13C ILV constant-time Carr-Purcell-Meiboom-Gill relaxation measurements experiments, we demonstrated that all four catalytically important loops-the WPD, Q, E, and substrate-binding loops-work in dynamic unity throughout the catalytic cycle of PTP1B. Thus, these data show that PTP1B activity is not controlled by a single functional element, but instead all key elements are dynamically coordinated. Together, these data provide the first fully comprehensive picture on how the validated drug target PTP1B functions.
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Affiliation(s)
- Kristiane R Torgeson
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Michael W Clarkson
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Ganesan Senthil Kumar
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA.
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15
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Ruddraraju KV, Aggarwal D, Niu C, Baker EA, Zhang RY, Wu L, Zhang ZY. Highly Potent and Selective N-Aryl Oxamic Acid-Based Inhibitors for Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. J Med Chem 2020; 63:9212-9227. [PMID: 32787087 DOI: 10.1021/acs.jmedchem.0c00302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tuberculosis is an infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb). Mtb protein tyrosine phosphatase B (mPTPB) is a virulence factor required for Mtb survival in host macrophages. Consequently, mPTPB represents an exciting target for tuberculosis treatment. Here, we identified N-phenyl oxamic acid as a highly potent and selective monoacid-based phosphotyrosine mimetic for mPTPB inhibition. SAR studies on the initial hit, compound 4 (IC50 = 257 nM), resulted in several highly potent inhibitors with IC50 values lower than 20 nM for mPTPB. Among them, compound 4t showed a Ki of 2.7 nM for mPTPB with over 4500-fold preference over 25 mammalian PTPs. Kinetic, molecular docking, and site-directed mutagenesis analyses confirmed these compounds as active site-directed reversible inhibitors of mPTPB. These inhibitors can reverse the altered host cell immune responses induced by the bacterial phosphatase. Furthermore, the inhibitors possess molecular weights <400 Da, log D7.4 < 2.5, topological polar surface area < 75, ligand efficiency > 0.43, and good aqueous solubility and metabolic stability, thus offering excellent starting points for further therapeutic development.
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Affiliation(s)
- Kasi Viswanatharaju Ruddraraju
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Devesh Aggarwal
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Congwei Niu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Erica Anne Baker
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Ruo-Yu Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Li Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
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16
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Kousaxidis A, Petrou A, Lavrentaki V, Fesatidou M, Nicolaou I, Geronikaki A. Aldose reductase and protein tyrosine phosphatase 1B inhibitors as a promising therapeutic approach for diabetes mellitus. Eur J Med Chem 2020; 207:112742. [PMID: 32871344 DOI: 10.1016/j.ejmech.2020.112742] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus is a metabolic disease characterized by high blood glucose levels and usually associated with several chronic pathologies. Aldose reductase and protein tyrosine phosphatase 1B enzymes have identified as two novel molecular targets associated with the onset and progression of type II diabetes and related comorbidities. Although many inhibitors against these enzymes have already found in the field of diabetic mellitus, the research for discovering more effective and selective agents with optimal pharmacokinetic properties continues. In addition, dual inhibition of these target proteins has proved as a promising therapeutic approach. A variety of diverse scaffolds are presented in this review for the future design of potent and selective inhibitors of aldose reductase and protein tyrosine phosphatase 1B based on the most important structural features of both enzymes. The discovery of novel dual aldose reductase and protein tyrosine phosphatase 1B inhibitors could be effective therapeutic molecules for the treatment of insulin-resistant type II diabetes mellitus. The methods used comprise a literature survey and X-ray crystal structures derived from Protein Databank (PDB). Despite the available therapeutic options for type II diabetes mellitus, the inhibitors of aldose reductase and protein tyrosine phosphatase 1B could be two promising approaches for the effective treatment of hyperglycemia and diabetes-associated pathologies. Due to the poor pharmacokinetic profile and low in vivo efficacy of existing inhibitors of both targets, the research turned to more selective and cell-permeable agents as well as multi-target molecules.
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Affiliation(s)
- Antonios Kousaxidis
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Anthi Petrou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Vasiliki Lavrentaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Maria Fesatidou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Ioannis Nicolaou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Athina Geronikaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece.
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17
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Puckett DL, Alquraishi M, Alani D, Chahed S, Donohoe D, Voy B, Whelan J, Bettaieb A. Zyflamend induces apoptosis in pancreatic cancer cells via modulation of the JNK pathway. Cell Commun Signal 2020; 18:126. [PMID: 32795297 PMCID: PMC7427957 DOI: 10.1186/s12964-020-00609-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Background Current pharmacological therapies and treatments targeting pancreatic neuroendocrine tumors (PNETs) have proven ineffective, far too often. Therefore, there is an urgent need for alternative therapeutic approaches. Zyflamend, a combination of anti-inflammatory herbal extracts, that has proven to be effective in various in vitro and in vivo cancer platforms, shows promise. However, its effects on pancreatic cancer, in particular, remain largely unexplored. Methods In the current study, we investigated the effects of Zyflamend on the survival of beta-TC-6 pancreatic insulinoma cells (β-TC6) and conducted a detailed analysis of the underlying molecular mechanisms. Results Herein, we demonstrate that Zyflamend treatment decreased cell proliferation in a dose-dependent manner, concomitant with increased apoptotic cell death and cell cycle arrest at the G2/M phase. At the molecular level, treatment with Zyflamend led to the induction of ER stress, autophagy, and the activation of c-Jun N-terminal kinase (JNK) pathway. Notably, pharmacological inhibition of JNK abrogated the pro-apoptotic effects of Zyflamend. Furthermore, Zyflamend exacerbated the effects of streptozotocin and adriamycin-induced ER stress, autophagy, and apoptosis. Conclusion The current study identifies Zyflamend as a potential novel adjuvant in the treatment of pancreatic cancer via modulation of the JNK pathway. Video abstract
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Affiliation(s)
- Dexter L Puckett
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Mohammed Alquraishi
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Dina Alani
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Samah Chahed
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Dallas Donohoe
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA
| | - Brynn Voy
- Tennessee Agricultural Experiment Station, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996-0840, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Jay Whelan
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA.,Tennessee Agricultural Experiment Station, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996-0840, USA
| | - Ahmed Bettaieb
- Department of Nutrition, University of Tennessee Knoxville, 1215 Cumberland Avenue, 229 Jessie Harris Building, Knoxville, TN, 37996-0840, USA. .,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996-0840, USA. .,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA.
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18
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Karimi M, Wu D, Wang Z, Shen Y. DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. Bioinformatics 2020; 35:3329-3338. [PMID: 30768156 DOI: 10.1093/bioinformatics/btz111] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/26/2018] [Accepted: 02/12/2019] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy and interpretability. RESULTS We present a seamless integration of domain knowledges and learning-based approaches. Under novel representations of structurally annotated protein sequences, a semi-supervised deep learning model that unifies recurrent and convolutional neural networks has been proposed to exploit both unlabeled and labeled data, for jointly encoding molecular representations and predicting affinities. Our representations and models outperform conventional options in achieving relative error in IC50 within 5-fold for test cases and 20-fold for protein classes not included for training. Performances for new protein classes with few labeled data are further improved by transfer learning. Furthermore, separate and joint attention mechanisms are developed and embedded to our model to add to its interpretability, as illustrated in case studies for predicting and explaining selective drug-target interactions. Lastly, alternative representations using protein sequences or compound graphs and a unified RNN/GCNN-CNN model using graph CNN (GCNN) are also explored to reveal algorithmic challenges ahead. AVAILABILITY AND IMPLEMENTATION Data and source codes are available at https://github.com/Shen-Lab/DeepAffinity. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mostafa Karimi
- Department of Electrical and Computer Engineering, College Station, TX, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, College Station, TX, USA
| | - Di Wu
- Department of Electrical and Computer Engineering, College Station, TX, USA
| | - Zhangyang Wang
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, College Station, TX, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, College Station, TX, USA
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19
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Abstract
Tyrosine phosphorylation is a critical component of signal transduction for multicellular organisms, particularly for pathways that regulate cell proliferation and differentiation. While tyrosine kinase inhibitors have become FDA-approved drugs, inhibitors of the other important components of these signaling pathways have been harder to develop. Specifically, direct phosphotyrosine (pTyr) isosteres have been aggressively pursued as inhibitors of Src homology 2 (SH2) domains and protein tyrosine phosphatases (PTPs). Medicinal chemists have produced many classes of peptide and small molecule inhibitors that mimic pTyr. However, balancing affinity with selectivity and cell penetration has made this an extremely difficult space for developing successful clinical candidates. This review will provide a comprehensive picture of the field of pTyr isosteres, from early beginnings to the current state and trajectory. We will also highlight the major protein targets of these medicinal chemistry efforts, the major classes of peptide and small molecule inhibitors that have been developed, and the handful of compounds which have been tested in clinical trials.
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Affiliation(s)
- Robert A Cerulli
- Cellular, Molecular and Developmental Biology Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
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20
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Wang Q, Fu XQ, Zheng QC. Exploring the allosteric mechanism of protein tyrosine phosphatase 1B by molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:4040-4047. [DOI: 10.1080/07391102.2019.1682049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Quan Wang
- Edmond H Fischer Signal Transduct Lab, College of Life Science, Jilin University, Changchun, People’s Republic Of China
| | - Xue-Qi Fu
- Edmond H Fischer Signal Transduct Lab, College of Life Science, Jilin University, Changchun, People’s Republic Of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People’s Republic Of China
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21
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Jung YJ, Miller DP, Perpich JD, Fitzsimonds ZR, Shen D, Ohshima J, Lamont RJ. Porphyromonas gingivalis Tyrosine Phosphatase Php1 Promotes Community Development and Pathogenicity. mBio 2019; 10:e02004-19. [PMID: 31551334 PMCID: PMC6759763 DOI: 10.1128/mbio.02004-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/23/2019] [Indexed: 01/17/2023] Open
Abstract
Protein-tyrosine phosphorylation in bacteria plays a significant role in multiple cellular functions, including those related to community development and virulence. Metal-dependent protein tyrosine phosphatases that belong to the polymerase and histindinol phosphatase (PHP) family are widespread in Gram-positive bacteria. Here, we show that Porphyromonas gingivalis, a Gram-negative periodontal pathogen, expresses a PHP protein, Php1, with divalent metal ion-dependent tyrosine phosphatase activity. Php1 tyrosine phosphatase activity was attenuated by mutation of conserved histidine residues that are important for the coordination of metal ions and by mutation of a conserved arginine residue, a key residue for catalysis in other bacterial PHPs. The php1 gene is located immediately downstream of the gene encoding the bacterial tyrosine (BY) kinase Ptk1, which was a substrate for Php1 in vitro Php1 rapidly caused the conversion of Ptk1 to a state of low tyrosine phosphorylation in the absence of discernible intermediate phosphoforms. Active Php1 was required for P. gingivalis exopolysaccharide production and for community development with the antecedent oral biofilm constituent Streptococcus gordonii under nutrient-depleted conditions. In contrast, the absence of Php1 had no effect on the ability of P. gingivalis to form monospecies biofilms. In vitro, Php1 enzymatic activity was resistant to the effects of the streptococcal secreted metabolites pABA and H2O2, which inhibited Ltp1, an enzyme in the low-molecular-weight (LMW) phosphotyrosine phosphatase family. Ptk1 reciprocally phosphorylated Php1 on tyrosine residues 159 and 161, which independently impacted phosphatase activity. Loss of Php1 rendered P. gingivalis nonvirulent in an animal model of periodontal disease. Collectively, these results demonstrate that P. gingivalis possesses active PHP and LMW tyrosine phosphatases, a unique configuration in Gram-negatives which may allow P. gingivalis to maintain phosphorylation/dephosphorylation homeostasis in multispecies communities. Moreover, Php1 contributes to the pathogenic potential of the organism.IMPORTANCE Periodontal diseases are among the most common infections of humans and are also associated with systemic inflammatory conditions. Colonization and pathogenicity of P. gingivalis are regulated by signal transduction pathways based on protein tyrosine phosphorylation and dephosphorylation. Here, we identify and characterize a novel component of the tyrosine (de)phosphorylation axis: a polymerase and histindinol phosphatase (PHP) family enzyme. This tyrosine phosphatase, designated Php1, was required for P. gingivalis community development with other oral bacteria, and in the absence of Php1 activity P. gingivalis was unable to cause disease in a mouse model of periodontitis. This work provides significant insights into the protein tyrosine (de)phosphorylation network in P. gingivalis, its adaptation to heterotypic communities, and its contribution to colonization and virulence.
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Affiliation(s)
- Young-Jung Jung
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - John D Perpich
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Zackary R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Daonan Shen
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Jun Ohshima
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
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22
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Varshney K, Gupta AK, Rawat A, Srivastava R, Mishra A, Saxena M, Srivastava AK, Jain S, Saxena AK. Synthesis,
SAR
and docking studies of substituted aryl phenylthiazolyl phenylcarboxamide as potential protein tyrosine phosphatase 1B (
PTP
1B) inhibitors. Chem Biol Drug Des 2019; 94:1378-1389. [DOI: 10.1111/cbdd.13515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/24/2019] [Accepted: 03/03/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Kanika Varshney
- Medicinal and Process Chemistry Division Central Drug Research Institute Lucknow India
- Department of Chemistry Lucknow University Lucknow India
| | - Amit K. Gupta
- Department of Integrative Biology and Pharmacology McGovern Medical School University of Texas Health Science Center at Houston Houston Texas
| | - Arun Rawat
- Biochemistry Division Central Drug Research Institute Lucknow India
| | - Rohit Srivastava
- Biochemistry Division Central Drug Research Institute Lucknow India
| | - Akansha Mishra
- Biochemistry Division Central Drug Research Institute Lucknow India
| | | | | | - Sudha Jain
- Department of Chemistry Lucknow University Lucknow India
| | - Anil K. Saxena
- Medicinal and Process Chemistry Division Central Drug Research Institute Lucknow India
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23
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Eleftheriou P, Geronikaki A, Petrou A. PTP1b Inhibition, A Promising Approach for the Treatment of Diabetes Type II. Curr Top Med Chem 2019; 19:246-263. [PMID: 30714526 DOI: 10.2174/1568026619666190201152153] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 01/07/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND Diabetes Mellitus (DM), is a metabolic disorder characterized by high blood glucose levels. The main types of diabetes mellitus are Diabetes mellitus type I, Diabetes mellitus type II, gestational diabetes and Diabetes of other etiology. Diabetes type II, the Non Insulin Dependent Type (NIDDM) is the most common type, characterized by the impairment in activation of the intracellular mechanism leading to the insertion and usage of glucose after interaction of insulin with its receptor, known as insulin resistance. Although, a number of drugs have been developed for the treatment of diabetes type II, their ability to reduce blood glucose levels is limited, while several side effects are also observed. Furthermore, none of the market drugs targets the enhancement of the action of the intracellular part of insulin receptor or recuperation of the glucose transport mechanism in GLUT4 dependent cells. The Protein Tyrosine Phosphatase (PTP1b) is the main enzyme involved in insulin receptor desensitization and has become a drug target for the treatment of Diabetes type II. Several PTP1b inhibitors have already been found, interacting with the binding site of the enzyme, surrounding the catalytic amino acid Cys215 and the neighboring area or with the allosteric site of the enzyme, placed at a distance of 20 Å from the active site, around Phe280. However, the research continues for finding more potent inhibitors with increased cell permeability and specificity. OBJECTIVE The aim of this review is to show the attempts made in developing of Protein Tyrosine Phosphatase (PTP1b) inhibitors with high potency, selectivity and bioavailability and to sum up the indications for favorable structural characteristics of effective PTP1b inhibitors. METHODS The methods used include a literature survey and the use of Protein Structure Databanks such as PuBMed Structure and RCSB and the tools they provide. CONCLUSION The research for finding PTP1b inhibitors started with the design of molecules mimicking the Tyrosine substrate of the enzyme. The study revealed that an aromatic ring connected to a polar group, which preferably enables hydrogen bond formation, is the minimum requirement for small inhibitors binding to the active site surrounding Cys215. Molecules bearing two hydrogen bond donor/acceptor (Hb d/a) groups at a distance of 8.5-11.5 Å may form more stable complexes, interacting simultaneously with a secondary area A2. Longer molecules with two Hb d/a groups at a distance of 17 Å or 19 Å may enable additional interactions with secondary sites (B and C) that confer stability as well as specificity. An aromatic ring linked to polar or Hb d/a moieties is also required for allosteric inhibitors. A lower distance between Hb d/a moieties, around 7.5 Å may favor allosteric interaction. Permanent inhibition of the enzyme by oxidation of the catalytic Cys215 has also been referred. Moreover, covalent modification of Cys121, placed near but not inside the catalytic pocket has been associated with permanent inhibition of the enzyme.
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Affiliation(s)
- Phaedra Eleftheriou
- Department of Medical Laboratory Studies, School of Health and Medical Care, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki 57400, Greece
| | - Athina Geronikaki
- Department of Pharmacy, School of Health, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Anthi Petrou
- Department of Pharmacy, School of Health, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
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The development of protein tyrosine phosphatase1B inhibitors defined by binding sites in crystalline complexes. Future Med Chem 2019; 10:2345-2367. [PMID: 30273014 DOI: 10.4155/fmc-2018-0089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Protein tyrosine phosphatase1B (PTP1B), a significant negative regulator in insulin and leptin signaling pathways, has emerged as a promising drug target for Type II diabetes mellitus and obesity. Numerous potent PTP1B inhibitors have been discovered within both academia and pharmaceutical industry. However, nearly all medicinal chemistry efforts have been severely hindered because a vast majority of them demonstrate poor membrane permeability and low-selectivity, especially over T-cell protein tyrosine phosphatase (TCPTP). To search the rules about the selectivity over TCPTP and membrane permeability of PTP1B inhibitors, based on the PTP1B/inhibitor crystal complexes, the development PTP1B inhibitors defined as AB, AC, ABC and ADC types have been concluded in the review.
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Inhibiting Protein Tyrosine Phosphatase 1B to Improve Regenerative Functions of Endothelial Cells. J Cardiovasc Pharmacol 2019; 71:59-64. [PMID: 28817487 DOI: 10.1097/fjc.0000000000000530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein tyrosine phosphatase-1B (PTP1B) is an important negative regulator of insulin receptor- and vascular endothelial growth factor receptor-dependent signalings in endothelial cells. Genetic or pharmacological inhibition of PTP1B has been shown to enhance endothelial cell proliferation and migration and increase nitric oxide production. In vivo, inhibiting PTP1B can reverse endothelial dysfunction, promote angiogenesis, and accelerate wound healing. Intense research is currently continuing in an effort to discover novel selective PTP1B inhibitors, primarily for treating insulin resistance. We propose that these drugs may also represent a new horizon for boosting the regenerative capacities of endothelial cells.
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Zhang H, Yang G, Chen J, Chen Z. Gewald Synthesis of 2-aminothiophenes on a Soluble Polymer-support. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.3184/0308234041639665] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A variety of polysubstituted thiophenes have been prepared via a solvent-free one-pot microwave assisted Gewald reaction using poly (ethylene glycol) as a soluble polymer support.
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Affiliation(s)
- Haiqing Zhang
- Faculty of Chemistry and Material Science, Hubei University, Wuhan, Hubei, 430062, P.R. China
| | - Guichun Yang
- Faculty of Chemistry and Material Science, Hubei University, Wuhan, Hubei, 430062, P.R. China
| | - Jianian Chen
- Faculty of Chemistry and Material Science, Hubei University, Wuhan, Hubei, 430062, P.R. China
| | - Zuxing Chen
- Faculty of Chemistry and Material Science, Hubei University, Wuhan, Hubei, 430062, P.R. China
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Hjortness MK, Riccardi L, Hongdusit A, Ruppe A, Zhao M, Kim EY, Zwart PH, Sankaran B, Arthanari H, Sousa MC, De Vivo M, Fox JM. Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation. Biochemistry 2018; 57:5886-5896. [PMID: 30169954 DOI: 10.1021/acs.biochem.8b00655] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein tyrosine phosphatases (PTPs) contribute to a striking variety of human diseases, yet they remain vexingly difficult to inhibit with uncharged, cell-permeable molecules; no inhibitors of PTPs have been approved for clinical use. This study uses a broad set of biophysical analyses to evaluate the use of abietane-type diterpenoids, a biologically active class of phytometabolites with largely nonpolar structures, for the development of pharmaceutically relevant PTP inhibitors. Results of nuclear magnetic resonance analyses, mutational studies, and molecular dynamics simulations indicate that abietic acid can inhibit protein tyrosine phosphatase 1B, a negative regulator of insulin signaling and an elusive drug target, by binding to its active site in a non-substrate-like manner that stabilizes the catalytically essential WPD loop in an inactive conformation; detailed kinetic studies, in turn, show that minor changes in the structures of abietane-type diterpenoids (e.g., the addition of hydrogens) can improve potency (i.e., lower IC50) by 7-fold. These findings elucidate a previously uncharacterized mechanism of diterpenoid-mediated inhibition and suggest, more broadly, that abietane-type diterpenoids are a promising source of structurally diverse-and, intriguingly, microbially synthesizable-molecules on which to base the design of new PTP-inhibiting therapeutics.
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Affiliation(s)
- Michael K Hjortness
- Department of Chemical and Biological Engineering , University of Colorado , 3415 Colorado Avenue , Boulder , Colorado 80303 , United States
| | - Laura Riccardi
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Akarawin Hongdusit
- Department of Chemical and Biological Engineering , University of Colorado , 3415 Colorado Avenue , Boulder , Colorado 80303 , United States
| | - Alex Ruppe
- Department of Chemical and Biological Engineering , University of Colorado , 3415 Colorado Avenue , Boulder , Colorado 80303 , United States
| | - Mengxia Zhao
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Edward Y Kim
- Department of Chemical and Biological Engineering , University of Colorado , 3415 Colorado Avenue , Boulder , Colorado 80303 , United States
| | - Peter H Zwart
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Marcelo C Sousa
- Department of Biochemistry , University of Colorado , 3415 Colorado Avenue , Boulder , Colorado 80303 , United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Jerome M Fox
- Department of Chemical and Biological Engineering , University of Colorado , 3415 Colorado Avenue , Boulder , Colorado 80303 , United States
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Carmichael JC, Yokota H, Craven RC, Schmitt A, Wills JW. The HSV-1 mechanisms of cell-to-cell spread and fusion are critically dependent on host PTP1B. PLoS Pathog 2018; 14:e1007054. [PMID: 29742155 PMCID: PMC5962101 DOI: 10.1371/journal.ppat.1007054] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/21/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023] Open
Abstract
All herpesviruses have mechanisms for passing through cell junctions, which exclude neutralizing antibodies and offer a clear path to neighboring, uninfected cells. In the case of herpes simplex virus type 1 (HSV-1), direct cell-to-cell transmission takes place between epithelial cells and sensory neurons, where latency is established. The spreading mechanism is poorly understood, but mutations in four different HSV-1 genes can dysregulate it, causing neighboring cells to fuse to produce syncytia. Because the host proteins involved are largely unknown (other than the virus entry receptor), we were intrigued by an earlier discovery that cells infected with wild-type HSV-1 will form syncytia when treated with salubrinal. A biotinylated derivative of this drug was used to pull down cellular complexes, which were analyzed by mass spectrometry. One candidate was a protein tyrosine phosphatase (PTP1B), and although it ultimately proved not to be the target of salubrinal, it was found to be critical for the mechanism of cell-to-cell spread. In particular, a highly specific inhibitor of PTP1B (CAS 765317-72-4) blocked salubrinal-induced fusion, and by itself resulted in a dramatic reduction in the ability of HSV-1 to spread in the presence of neutralizing antibodies. The importance of this phosphatase was confirmed in the absence of drugs by using PTP1B-/- cells. Importantly, replication assays showed that virus titers were unaffected when PTP1B was inhibited or absent. Only cell-to-cell spread was altered. We also examined the effects of salubrinal and the PTP1B inhibitor on the four Syn mutants of HSV-1, and strikingly different responses were found. That is, both drugs individually enhanced fusion for some mutants and reduced fusion for others. PTP1B is the first host factor identified to be specifically required for cell-to-cell spread, and it may be a therapeutic target for preventing HSV-1 reactivation disease. It is estimated that 67% of the global population is infected with herpes simplex virus type 1 (HSV-1). This virus resides in sensory neurons in a quiescent state but periodically reactivates, producing virus particles that travel down the axon to infect epithelial cells of the skin, where it can be transmitted to additional people. To avoid neutralizing antibodies, herpesviruses have evolved mechanisms for moving directly from one cell to another through their sites of intimate contact; however, the mechanism of cell-to-cell spread is poorly understood. Studies of HSV-1 mutants have implicated numerous viral proteins, but the necessary cellular factors are unknown except for the one that the virus uses to enter cells. Our experiments have identified a cellular enzyme (PTP1B, a tyrosine phosphatase) that is dispensable for the production of infectious virions but is critically important for the cell-to-cell spreading mechanism. Promising drugs targeting PTP1B have already been tested in early clinical trials for possible treatment of obesity and type-2 diabetes, and thus, our study may have immediate utility for attenuating HSV-1 reactivation disease in immunocompromised patients.
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Affiliation(s)
- Jillian C. Carmichael
- Department of Microbiology and Immunology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, United States of America
| | - Hiroki Yokota
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Rebecca C. Craven
- Department of Microbiology and Immunology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, United States of America
| | - Anthony Schmitt
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - John W. Wills
- Department of Microbiology and Immunology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail:
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29
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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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Choy MS, Li Y, Machado LESF, Kunze MBA, Connors CR, Wei X, Lindorff-Larsen K, Page R, Peti W. Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery. Mol Cell 2017; 65:644-658.e5. [PMID: 28212750 DOI: 10.1016/j.molcel.2017.01.014] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/07/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022]
Abstract
Protein function originates from a cooperation of structural rigidity, dynamics at different timescales, and allostery. However, how these three pillars of protein function are integrated is still only poorly understood. Here we show how these pillars are connected in Protein Tyrosine Phosphatase 1B (PTP1B), a drug target for diabetes and cancer that catalyzes the dephosphorylation of numerous substrates in essential signaling pathways. By combining new experimental and computational data on WT-PTP1B and ≥10 PTP1B variants in multiple states, we discovered a fundamental and evolutionarily conserved CH/π switch that is critical for positioning the catalytically important WPD loop. Furthermore, our data show that PTP1B uses conformational and dynamic allostery to regulate its activity. This shows that both conformational rigidity and dynamics are essential for controlling protein activity. This connection between rigidity and dynamics at different timescales is likely a hallmark of all enzyme function.
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Affiliation(s)
- Meng S Choy
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Yang Li
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Luciana E S F Machado
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Micha B A Kunze
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark, Brown University, Providence, RI 02912, USA
| | - Christopher R Connors
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Xingyu Wei
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Kresten Lindorff-Larsen
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark, Brown University, Providence, RI 02912, USA
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA; Department of Chemistry, Brown University, Providence, RI 02912, USA.
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31
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Meng G, Zheng M, Wang M, Tong J, Ge W, Zhang J, Zheng A, Li J, Gao L, Li J. Design and synthesis of new potent PTP1B inhibitors with the skeleton of 2-substituted imino-3-substituted-5-heteroarylidene-1,3-thiazolidine-4-one: Part I. Eur J Med Chem 2016; 122:756-769. [PMID: 27526040 DOI: 10.1016/j.ejmech.2016.05.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/26/2016] [Accepted: 05/26/2016] [Indexed: 11/19/2022]
Abstract
A new series of 2-substituted imino-3-substituted-5- heteroarylidene-1,3-thiazolidine-4-ones as the potent bidentate PTP1B inhibitors were designed and synthesized in this paper. All of the new compounds were characterized and identified by spectra analysis. The biological screening test against PTP1B showed that some of these compounds have the positive inhibitory activity against PTP1B. The activity of the compounds with 5-substituted pyrrole on 5-postion of 1,3-thiazolidine-4-one are more potent than that of those compounds with 5-substituted pyridine group. Compound 14b, 14h and 14i showed IC50 values of 8.66 μM, 6.83 μM and 6.09 μM against PTP1B, respectively. Docking analysis of these active compounds with PTP1B showed the possible interaction modes of these biheterocyclic compounds with the active sites of PTP1B. The inhibition tests against oncogenetic CDC25B were also conducted on this set of compounds to evaluate the selectivity and possible anti-neoplastic activity. Compound 14b also showed the lowest IC50 of 1.66 μM against CDC25B among all the possible inhibitors, including 14g, 14h, 14i and 15c. Some pharmacological parameters including VolSurf, steric and electric descriptors of all the compounds were calculated to give some hints about the relative relationship with the biological activity. The result of this study might give some light on designing the possible anti-cancer drugs targeting at phosphatases. The most active compound 14i might be used as the lead compound for further structure modification of the new low molecular weight PTP1B inhibitors with the N-containing heterocyclic skeleton.
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Affiliation(s)
- Ge Meng
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China.
| | - Meilin Zheng
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Mei Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Jing Tong
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Weijuan Ge
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Jiehe Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi, 710061, PR China
| | - Aqun Zheng
- School of Science, Xi'an Jiaotong University, No. 28, Xianning West Road, Xi'an, Shaanxi, 710049, PR China
| | - Jingya Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Lixin Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
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Ghattas MA, Raslan N, Sadeq A, Al Sorkhy M, Atatreh N. Druggability analysis and classification of protein tyrosine phosphatase active sites. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:3197-3209. [PMID: 27757011 PMCID: PMC5053377 DOI: 10.2147/dddt.s111443] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, UAE
| | - Noor Raslan
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, UAE
| | - Asil Sadeq
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, UAE
| | - Mohammad Al Sorkhy
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, UAE
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, UAE
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Shen Y, Radhakrishnan ML, Tidor B. Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition. Proteins 2015; 83:351-72. [PMID: 25410041 PMCID: PMC4829108 DOI: 10.1002/prot.24730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/14/2014] [Accepted: 11/06/2014] [Indexed: 11/16/2022]
Abstract
Molecular recognition is central to biology and ranges from highly selective to broadly promiscuous. The ability to modulate specificity at will is particularly important for drug development, and discovery of mechanisms contributing to binding specificity is crucial for our basic understanding of biology and for applications in health care. In this study, we used computational molecular design to create a large dataset of diverse small molecules with a range of binding specificities. We then performed structural, energetic, and statistical analysis on the dataset to study molecular mechanisms of achieving specificity goals. The work was done in the context of HIV‐1 protease inhibition and the molecular designs targeted a panel of wild‐type and drug‐resistant mutant HIV‐1 protease structures. The analysis focused on mechanisms for promiscuous binding to bind robustly even to resistance mutants. Broadly binding inhibitors tended to be smaller in size, more flexible in chemical structure, and more hydrophobic in nature compared to highly selective ones. Furthermore, structural and energetic analyses illustrated mechanisms by which flexible inhibitors achieved binding; we found ligand conformational adaptation near mutation sites and structural plasticity in targets through torsional flips of asymmetric functional groups to form alternative, compensatory packing interactions or hydrogen bonds. As no inhibitor bound to all variants, we designed small cocktails of inhibitors to do so and discovered that they often jointly covered the target set through mechanistic complementarity. Furthermore, using structural plasticity observed in experiments, and potentially in simulations, is suggested to be a viable means of designing adaptive inhibitors that are promiscuous binders. Proteins 2015; 83:351–372. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Yang Shen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Present address:
Center for Bioinformatics and Genomic Systems EngineeringDepartment of Electrical and Computer EngineeringTexas A&M UniversityCollege StationTexas77843
| | | | - Bruce Tidor
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMassachusetts02139
- Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeMassachusetts02139
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Du Y, Ling H, zhang M, Shen J, Li Q. Discovery of novel, potent, selective and cellular active ADC type PTP1B inhibitors via fragment-docking-oriented de novel design. Bioorg Med Chem 2015; 23:4891-4898. [DOI: 10.1016/j.bmc.2015.05.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 12/17/2022]
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Krishnan N, Krishnan K, Connors CR, Choy MS, Page R, Peti W, Van Aelst L, Shea SD, Tonks NK. PTP1B inhibition suggests a therapeutic strategy for Rett syndrome. J Clin Invest 2015. [PMID: 26214522 DOI: 10.1172/jci80323] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The X-linked neurological disorder Rett syndrome (RTT) presents with autistic features and is caused primarily by mutations in a transcriptional regulator, methyl CpG-binding protein 2 (MECP2). Current treatment options for RTT are limited to alleviating some neurological symptoms; hence, more effective therapeutic strategies are needed. We identified the protein tyrosine phosphatase PTP1B as a therapeutic candidate for treatment of RTT. We demonstrated that the PTPN1 gene, which encodes PTP1B, was a target of MECP2 and that disruption of MECP2 function was associated with increased levels of PTP1B in RTT models. Pharmacological inhibition of PTP1B ameliorated the effects of MECP2 disruption in mouse models of RTT, including improved survival in young male (Mecp2-/y) mice and improved behavior in female heterozygous (Mecp2-/+) mice. We demonstrated that PTP1B was a negative regulator of tyrosine phosphorylation of the tyrosine kinase TRKB, the receptor for brain-derived neurotrophic factor (BDNF). Therefore, the elevated PTP1B that accompanies disruption of MECP2 function in RTT represents a barrier to BDNF signaling. Inhibition of PTP1B led to increased tyrosine phosphorylation of TRKB in the brain, which would augment BDNF signaling. This study presents PTP1B as a mechanism-based therapeutic target for RTT, validating a unique strategy for treating the disease by modifying signal transduction pathways with small-molecule drugs.
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Screening of novel inhibitors targeting lactate dehydrogenase A via four molecular docking strategies and dynamics simulations. J Mol Model 2015; 21:133. [PMID: 25934158 DOI: 10.1007/s00894-015-2675-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/01/2015] [Indexed: 01/14/2023]
Abstract
Lactate dehydrogenase A (LDHA) is a metabolic enzyme which catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway, thus playing key roles in aerobic glycolysis. The inhibition of LDHA by small molecules has become an attractive strategy for anticancer therapy in recent years. However, very few LDHA inhibitors have been reported, even though a great deal of effort has directed into identifying LDHA inhibitors using structure-based approaches. Therefore, high-throughput and high-accuracy screening approaches are still urgently needed in order to target LDHA effectively. In the present work, after establishing that our docking strategies performed well using test datasets, we screened 32791 Specs products for their docking scores with the substrate-binding pocket and, separately, the cofactor-binding pocket of LDHA. We subsequently identified 76 hits (i.e., ligands that show low docking scores) for the cofactor-binding pocket and 27 hits for the substrate-binding pocket. Two representative compounds, ZINC20036549 and ZINC19369718, were then chosen for further MD simulation analysis, and we found that these compounds maintained their inhibitory activity during the MD simulations. Meanwhile, we found that ZINC19369718 interacts with a novel binding site close to the active site, and that this interaction may inhibit the catalytic activity of LDHA. Together, these results offer not only a new paradigm for identifying Specs drug-like products for novel therapeutic use but they also provide further opportunity to adopt LDHA inhibition as a strategy for cancer therapy.
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Ghattas MA, Atatreh N, Bichenkova EV, Bryce RA. Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening. J Mol Graph Model 2014; 52:114-23. [PMID: 25038507 DOI: 10.1016/j.jmgm.2014.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/23/2014] [Accepted: 06/26/2014] [Indexed: 11/28/2022]
Abstract
Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain 64141, United Arab Emirates
| | - Elena V Bichenkova
- Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Richard A Bryce
- Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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Beales ILP, Garcia-Morales C, Ogunwobi OO, Mutungi G. Adiponectin inhibits leptin-induced oncogenic signalling in oesophageal cancer cells by activation of PTP1B. Mol Cell Endocrinol 2014; 382:150-158. [PMID: 23994026 DOI: 10.1016/j.mce.2013.08.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/21/2013] [Accepted: 08/21/2013] [Indexed: 01/05/2023]
Abstract
Obesity is characterised by hyperleptinaemia and hypoadiponectinaemia and these metabolic abnormalities may contribute to the progression of several obesity-associated cancers including oesophageal adenocarcinoma (OAC). We have examined the effects of leptin and adiponectin on OE33 OAC cells. Leptin stimulated proliferation, invasion and migration and inhibited apoptosis in a STAT3-dependant manner. Leptin-stimulated MMP-2 secretion in a partly STAT3-dependent manner and MMP-9 secretion via a STAT3-independent pathway. Adiponectin inhibited leptin-induced proliferation, migration, invasion, MMP secretion and reduced the anti-apoptotic effects: these effects of adiponectin were ameliorated by both a non-specific tyrosine phosphatase inhibitor and a specific PTP1B inhibitor. Adiponectin reduced leptin-stimulated JAK2 activation and STAT3 transcriptional activity in a PTP1B-sensitive manner and adiponectin increased both PTP1B protein and activity. We conclude that adiponectin restrains leptin-induced signalling and pro-carcinogenic behaviour by inhibiting the early events in leptin-induced signal transduction by activating PTP1B. Relative adiponectin deficiency in obesity may contribute to the promotion of OAC.
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Affiliation(s)
- Ian L P Beales
- Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich NR4 7UZ, UK; Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Carla Garcia-Morales
- Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich NR4 7TJ, UK
| | - Olorunseun O Ogunwobi
- Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich NR4 7TJ, UK
| | - Gabriel Mutungi
- Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich NR4 7TJ, UK
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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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40
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El-Saghier AMM, Akkurt M, Mohamed SK, Horton PN, Albayati MR. Ethyl 3-amino-5-anilino-4-cyano-thio-phene-2-carboxyl-ate. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o1244-o1245. [PMID: 24109334 PMCID: PMC3793747 DOI: 10.1107/s1600536813018734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 06/02/2023]
Abstract
In the title compound, C14H13N3O2S, the dihedral angle between the thio-phene and phenyl rings is 24.95 (8)°. The mol-ecular structure is consolidated by intra-molecular N-H⋯O and C-H⋯S inter-actions. The crystal structure features N-H⋯N and N-H⋯O hydrogen bonds forming centrosymmetric R 2 (2)(12) dimers, which are linked into a two-dimensional network parallel to (011) with an S(6)R 2 (2) S(6) motif. In addition, π-π stacking inter-actions [centroid-centroid distance = 3.7013 (12) Å] occur between the thio-phene and phenyl rings of adjacent mol-ecules.
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Affiliation(s)
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey
| | - Shaaban K. Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England
- Chemistry Department, Faculty of Science, Mini University, 61519 El-Minia, Egypt
| | - Peter N. Horton
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, England
| | - Mustafa R. Albayati
- Kirkuk University, College of Science, Department of Chemistry, Kirkuk, Iraq
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41
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Haftchenary S, Ball DP, Aubry I, Landry M, Shahani VM, Fletcher S, Page BDG, Jouk AO, Tremblay ML, Gunning PT. Identification of a potent salicylic acid-based inhibitor of tyrosine phosphatase PTP1B. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00011g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A screen of a library of diverse small-molecules against a subset of phosphatases identified 7b and 7c, which potently inhibit TC-PTP, PTPσ and PTP1B with no inhibition of PTP-LAR, PRL2 A/S, MKPX or papain.
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Affiliation(s)
| | - Daniel P. Ball
- Department of Chemistry
- University of Toronto
- Mississauga
- Canada
| | - Isabelle Aubry
- McGill Goodman Cancer Research Centre and Department of Biochemistry
- McGill University
- Montreal
- Canada
| | - Melissa Landry
- McGill Goodman Cancer Research Centre and Department of Biochemistry
- McGill University
- Montreal
- Canada
| | | | - Steven Fletcher
- Department of Chemistry
- University of Toronto
- Mississauga
- Canada
| | | | | | - Michel L. Tremblay
- McGill Goodman Cancer Research Centre and Department of Biochemistry
- McGill University
- Montreal
- Canada
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42
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Store-operated Ca2+ entry in hippocampal neurons: Regulation by protein tyrosine phosphatase PTP1B. Cell Calcium 2012; 53:125-38. [PMID: 23218930 DOI: 10.1016/j.ceca.2012.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 10/12/2012] [Accepted: 11/04/2012] [Indexed: 11/20/2022]
Abstract
Store operated Ca(2+) entry (SOCE) replenishes intracellular Ca(2+) stores and activates a number of intracellular signalling pathways. Whilst several molecular components forming store operated Ca(2+) channels (SOCC) have been identified, their modulation in neurons remains poorly understood. Here, we extend on our previous findings and show that neuronal SOCE is modulated by tyrosine phosphorylation. Cyclopiazonic acid induced SOCE was characterised in hippocampal cultures derived from forebrain specific protein tyrosine phosphatase 1B knockout (PTP1B KO) mice and wild type (WT) litter mates using Fura-2 Ca(2+) imaging. PTP1B KO cultures expressed elevated SOCE relative to WT cultures without changes in cytoplasmic Ca(2+) homeostasis or depolarisation-induced Ca(2+) influx. WT and PTP1B KO cultures displayed similar pharmacological sensitivities towards the SOCE inhibitors gadolinium and 2-aminoethoxydiphenyl borate, as well as the tyrosine kinase inhibitor Ag126 indicating an augmentation of native SOCCs by PTP1B. Following store depletion WT culture homogenates showed heightened phospho-tyrosine levels, an increase in Src tyrosine kinase activation and two minor PTP1B species. These data suggest tyrosine phosphorylation gating SOCE, and implicate PTP1B as a key regulatory enzyme. The involvement of PTP1B in SOCE and its relation to SOCC components and mechanism of regulation are discussed.
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43
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Dai HL, Gao LX, Yang Y, Li JY, Cheng JG, Li J, Wen R, Peng YQ, Zheng JB. Discovery of di-indolinone as a novel scaffold for protein tyrosine phosphatase 1B inhibitors. Bioorg Med Chem Lett 2012; 22:7440-3. [DOI: 10.1016/j.bmcl.2012.10.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 10/27/2022]
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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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45
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Lubben T, Clampit J, Stashko M, Trevillyan J, Jirousek MR. In vitro enzymatic assays of protein tyrosine phosphatase 1B. ACTA ACUST UNITED AC 2012; Chapter 3:Unit3.8. [PMID: 21959757 DOI: 10.1002/0471141755.ph0308s13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many hormone or growth factor receptors signal via the activation of protein-tyrosine kinases and phosphatases. Alteration of the phosphorylation state of tyrosine residues in certain proteins can directly regulate enzyme activity or cause formation of protein complexes necessary for transducing intracellular signals. Genetic and biochemical evidence also implicates protein-tyrosine phosphatases in several disease processes, including negative regulation of insulin receptor signaling at the level of the insulin receptor and perhaps in signaling at the IRS-1 level. The expression of protein tyrosine phosphatase-1B (PTP1B) is elevated in muscle and adipose tissue in insulin-resistant states both in man and rodents suggesting that PTP1B may play a role in the insulin-resistant state associated with diabetes and obesity. As described in this unit, PTP1B activity can be determined with the small molecule substrate, p-nitrophenyl phosphate (pNPP), in which the cleavage of the phosphate results in production of p-nitrophenol (pNP) and an increase in absorbance at 405 nm. Alternatively, PTP1B activity can be measured as described using model phosphotyrosyl-containing peptide substrates in which the release of free phosphate from the peptide is determined using a malachite green colorimetric assay.
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Affiliation(s)
- T Lubben
- Abbott Laboratories, Abbott Park, IL, USA
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46
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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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47
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Lu L, Gao X, Zhu M, Wang S, Wu Q, Xing S, Fu X, Liu Z, Guo M. Exploration of biguanido-oxovanadium complexes as potent and selective inhibitors of protein tyrosine phosphatases. Biometals 2012; 25:599-610. [PMID: 22547055 DOI: 10.1007/s10534-012-9548-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
Abstract
The inhibitory effects of three biguanido-oxovanadium complexes ([VO(L(1-3))(2)]·nH(2)O: HL(1) = metformin, HL(2) = phenformin, HL(3) = moroxydine) against four protein tyrosine phosphatases (PTPs) and an alkaline phosphatase (ALP) were investigated. The complexes display strong inhibition against PTP1B and TCPTP (IC(50), 80-160 nM), a bit weaker inhibition against HePTP (IC(50), 190-410 nM) and SHP-1(IC(50), 0.8-3.3 μM) and much weaker inhibition against ALP (IC(50), 17-35 μM). Complex 3 is about twofold less potent against PTP1B, TCPTP and HePTP than complexes 1 and 2, while complex 2 inhibits SHP-1 more strongly (about three to fourfold) than the other two complexes. These results suggest that the structures of the ligands slightly influence the potency and selectivity against PTPs. The complexes inhibit PTP1B and ALP with a typical competitive type.
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Affiliation(s)
- Liping Lu
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Shanxi University, Taiyuan 030006, Shanxi, People's Republic of China
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48
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Affiliation(s)
- David J Huggins
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom.
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49
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Sheriff S, Beno BR, Zhai W, Kostich WA, McDonnell PA, Kish K, Goldfarb V, Gao M, Kiefer SE, Yanchunas J, Huang Y, Shi S, Zhu S, Dzierba C, Bronson J, Macor JE, Appiah KK, Westphal RS, O’Connell J, Gerritz SW. Small Molecule Receptor Protein Tyrosine Phosphatase γ (RPTPγ) Ligands That Inhibit Phosphatase Activity via Perturbation of the Tryptophan–Proline–Aspartate (WPD) Loop. J Med Chem 2011; 54:6548-62. [DOI: 10.1021/jm2003766] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Steven Sheriff
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Brett R. Beno
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Weixu Zhai
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Walter A. Kostich
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Patricia A. McDonnell
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Kevin Kish
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Valentina Goldfarb
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Mian Gao
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Susan E. Kiefer
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Joseph Yanchunas
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Yanling Huang
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shuhao Shi
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shirong Zhu
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Carolyn Dzierba
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Joanne Bronson
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - John E. Macor
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kingsley K. Appiah
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ryan S. Westphal
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jonathan O’Connell
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Samuel W. Gerritz
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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Böttcher J, Jestel A, Kiefersauer R, Krapp S, Nagel S, Steinbacher S, Steuber H. Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology. Methods Enzymol 2011; 493:61-89. [PMID: 21371587 DOI: 10.1016/b978-0-12-381274-2.00003-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
In the past two decades, fragment-based approaches have evolved as a predominant strategy in lead discovery. The availability of structural information on the interaction geometries of binding fragments is key to successful structure-guided fragment-to-lead evolution. In this chapter, we illustrate methodological advances for protein-fragment crystal structure generation in order to offer general lessons on the importance of fragment properties and the most appropriate crystallographic setup to evaluate them. We analyze elaborate protocols, methods, and clues applied to challenging complex formation projects. The results should assist medicinal chemists to select the most promising targets and strategies for fragment-based crystallography as well as provide a tutorial to structural biologists who attempt to determine protein-fragment structures.
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Affiliation(s)
- Jark Böttcher
- Proteros biostructures GmbH, Am Klopferspitz 19, Martinsried, Germany
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