1
|
Ross MO, Xie Y, Owyang RC, Ye C, Zbihley ONP, Lyu R, Wu T, Wang P, Karginova O, Olopade OI, Zhao M, He C. PTPN2 copper-sensing rapidly relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555401. [PMID: 37693440 PMCID: PMC10491225 DOI: 10.1101/2023.08.29.555401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Fluxes in human intra- and extracellular copper levels recently garnered attention for roles in cellular signaling, including affecting levels of the signaling molecule cyclic adenosine monophosphate (cAMP). We herein applied an unbiased temporal evaluation of the whole-genome transcriptional activities modulated by fluctuations in copper levels to identify the copper sensor proteins responsible for driving these activities. We found that fluctuations in physiologically-relevant copper levels rapidly modulate EGFR/MAPK/ERK signal transduction and activation of the transcription factor cAMP response element-binding protein (CREB). Both intracellular and extracellular assays support Cu 1+ inhibition of the EGFR-phosphatase PTPN2 (and potentially the homologous PTPN1)-via direct ligation to the PTPN2 active site cysteine side chain-as the underlying mechanism of copper-stimulated EGFR signal transduction activation. Depletion of copper represses this signaling pathway. We additionally show i ) copper supplementation drives transcriptional repression of the copper importer CTR1 and ii ) CREB activity is inversely correlated with CTR1 expression. In summary, our study reveals PTPN2 as a physiological copper sensor and defines a regulatory mechanism linking feedback control of copper-stimulated MAPK/ERK/CREB-signaling and CTR1 expression, thereby uncovering a previously unrecognized link between copper levels and cellular signal transduction.
Collapse
|
2
|
Friedman AJ, Liechty ET, Kramer L, Sarkar A, Fox JM, Shirts MR. Allosteric Inhibition of PTP1B by a Nonpolar Terpenoid. J Phys Chem B 2022; 126:8427-8438. [PMID: 36223525 PMCID: PMC10040085 DOI: 10.1021/acs.jpcb.2c05423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are promising drug targets for treating a wide range of diseases such as diabetes, cancer, and neurological disorders, but their conserved active sites have complicated the design of selective therapeutics. This study examines the allosteric inhibition of PTP1B by amorphadiene (AD), a terpenoid hydrocarbon that is an unusually selective inhibitor. Molecular dynamics (MD) simulations carried out in this study suggest that AD can stably sample multiple neighboring sites on the allosterically influential C-terminus of the catalytic domain. Binding to these sites requires a disordered α7 helix, which stabilizes the PTP1B-AD complex and may contribute to the selectivity of AD for PTP1B over TCPTP. Intriguingly, the binding mode of AD differs from that of the most well-studied allosteric inhibitor of PTP1B. Indeed, biophysical measurements and MD simulations indicate that the two molecules can bind simultaneously. Upon binding, both inhibitors destabilize the α7 helix by disrupting interactions at the α3-α7 interface and prevent the formation of hydrogen bonds that facilitate closure of the catalytically essential WPD loop. These findings indicate that AD is a promising scaffold for building allosteric inhibitors of PTP1B and illustrate, more broadly, how unfunctionalized terpenoids can engage in specific interactions with protein surfaces.
Collapse
Affiliation(s)
- Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Evan T Liechty
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Levi Kramer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Ankur Sarkar
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| |
Collapse
|
3
|
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.
Collapse
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:
| |
Collapse
|
4
|
Nayek A, Ahmed ME, Samanta S, Dinda S, Patra S, Dey SG, Dey A. Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling. J Am Chem Soc 2022; 144:8402-8429. [PMID: 35503922 DOI: 10.1021/jacs.2c01842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH+/ne-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH+/ne- reactions. Such control can allow functional modeling of hydrogenases (H+ + e- → 1/2 H2), cytochrome c oxidase (O2 + 4 e- + 4 H+ → 2 H2O), monooxygenases (RR'CH2 + O2 + 2 e- + 2 H+ → RR'CHOH + H2O) and dioxygenases (S + O2 → SO2; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.
Collapse
Affiliation(s)
- Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Md Estak Ahmed
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Souvik Dinda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| |
Collapse
|
5
|
Rath P, Ranjan A, Ghosh A, Chauhan A, Gurnani M, Tuli HS, Habeeballah H, Alkhanani MF, Haque S, Dhama K, Verma NK, Jindal T. Potential Therapeutic Target Protein Tyrosine Phosphatase-1B for Modulation of Insulin Resistance with Polyphenols and Its Quantitative Structure–Activity Relationship. Molecules 2022; 27:molecules27072212. [PMID: 35408611 PMCID: PMC9000704 DOI: 10.3390/molecules27072212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
The increase in the number of cases of type 2 diabetes mellitus (T2DM) and the complications associated with the side effects of chemical/synthetic drugs have raised concerns about the safety of the drugs. Hence, there is an urgent need to explore and identify natural bioactive compounds as alternative drugs. Protein tyrosine phosphatase 1B (PTP1B) functions as a negative regulator and is therefore considered as one of the key protein targets modulating insulin signaling and insulin resistance. This article deals with the screening of a database of polyphenols against PTP1B activity for the identification of a potential inhibitor. The research plan had two clear objectives. Under first objective, we conducted a quantitative structure–activity relationship analysis of flavonoids with PTP1B that revealed the strongest correlation (R2 = 93.25%) between the number of aromatic bonds (naro) and inhibitory concentrations (IC50) of PTP1B. The second objective emphasized the binding potential of the selected polyphenols against the activity of PTP1B using molecular docking, molecular dynamic (MD) simulation and free energy estimation. Among all the polyphenols, silydianin, a flavonolignan, was identified as a lead compound that possesses drug-likeness properties, has a higher negative binding energy of −7.235 kcal/mol and a pKd value of 5.2. The free energy-based binding affinity (ΔG) was estimated to be −7.02 kcal/mol. MD simulation revealed the stability of interacting residues (Gly183, Arg221, Thr263 and Asp265). The results demonstrated that the identified polyphenol, silydianin, could act as a promising natural PTP1B inhibitor that can modulate the insulin resistance.
Collapse
Affiliation(s)
- Prangya Rath
- Amity Institute of Environmental Sciences, Amity University, Noida 201303, India; (P.R.); (M.G.)
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
- Correspondence: (A.R.); (A.G.); Tel.: +91-999-090-7571 (A.R.); +91-967-862-9146 (A.G.)
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati 781014, India
- Correspondence: (A.R.); (A.G.); Tel.: +91-999-090-7571 (A.R.); +91-967-862-9146 (A.G.)
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida 201303, India; (A.C.); (T.J.)
| | - Manisha Gurnani
- Amity Institute of Environmental Sciences, Amity University, Noida 201303, India; (P.R.); (M.G.)
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, India;
| | - Hamza Habeeballah
- Faculty of Applied Medical Sciences, King Abdulaziz University, Rabigh Branch, Rabigh 25732, Saudi Arabia;
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Bursa Uludağ University Görükle Campus, Nilüfer 16059, Turkey
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India;
| | - Naval Kumar Verma
- Homeopathy, Ministry of Ayush, Ayush Bhawan, B Block, GPO Complex INA, New Delhi 110023, India;
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida 201303, India; (A.C.); (T.J.)
| |
Collapse
|
6
|
Cornejo NR, Amofah B, Lipinski A, Langlais PR, Ghosh I, Jewett JC. Direct Intracellular Delivery of Benzene Diazonium Ions As Observed by Increased Tyrosine Phosphorylation. Biochemistry 2022; 61:656-664. [PMID: 35302352 PMCID: PMC9203130 DOI: 10.1021/acs.biochem.1c00820] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A challenge within the field of bioconjugation is developing probes to uncover novel information on proteins and other biomolecules. Intracellular delivery of these probes offers the promise of giving relevant context to this information, and these probes can serve as hypothesis-generating tools within complex systems. Leveraging the utility of triazabutadiene chemistry, herein, we discuss the development of a probe that undergoes reduction-mediated deprotection to rapidly deliver a benzene diazonium ion (BDI) into cells. The intracellular BDI resulted in an increase in global tyrosine phosphorylation levels. Seeing phosphatase dysregulation as a potential source of this increase, a tyrosine phosphatase (PTP1B) was tested and shown to be both inhibited and covalently modified by the BDI. In addition to the expected azobenzene formation at tyrosine side chains, key reactive histidine residues were also modified.
Collapse
Affiliation(s)
- Natasha R Cornejo
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Bismark Amofah
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Austin Lipinski
- Department of Medicine, Division of Endocrinology, University of Arizona College of Medicine, Tucson, Arizona 85721, United States
| | - Paul R Langlais
- Department of Medicine, Division of Endocrinology, University of Arizona College of Medicine, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - John C Jewett
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| |
Collapse
|
7
|
Structure Revision and Protein Tyrosine Phosphatase Inhibitory Activity of Drazepinone. Mar Drugs 2021; 19:md19120714. [PMID: 34940713 PMCID: PMC8708580 DOI: 10.3390/md19120714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/29/2022] Open
Abstract
From the marine-derived fungus Penicillium sumatrense (Trichocomaceae), a pair of enantiomers [(+)-1 and (−)-1] were isolated with identical 1D NMR data to drazepinone, which was originally reported to have a trisubstituted naphthofuroazepinone skeleton. In this study, we confirmed the structures of the two enantiomers as drazepinone and revised their structures by detailed analysis of extensive 2D NMR data and a comparison of the calculated 13C chemical shifts, ECD, VCD, and ORD spectra with those of the experiment ones. (+)-1 and (−)-1 were evaluated for their PTP inhibitory activity in vitro. (−)-1 showed selective PTP inhibitory activity against PTP1B and TCPTP with IC50 values of 1.56 and 12.5 μg/mL, respectively.
Collapse
|
8
|
Elhassan RM, Hou X, Fang H. Recent advances in the development of allosteric protein tyrosine phosphatase inhibitors for drug discovery. Med Res Rev 2021; 42:1064-1110. [PMID: 34791703 DOI: 10.1002/med.21871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 09/26/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023]
Abstract
Protein tyrosine phosphatases (PTPs) superfamily catalyzes tyrosine de-phosphorylation which affects a myriad of cellular processes. Imbalance in signal pathways mediated by PTPs has been associated with development of many human diseases including cancer, metabolic, and immunological diseases. Several compelling evidence suggest that many members of PTP family are novel therapeutic targets. However, the clinical development of conventional PTP-based active-site inhibitors originally was hampered by the poor selectivity and pharmacokinetic properties. In this regard, PTPs has been widely dismissed as "undruggable." Nonetheless, allosteric modulation has become increasingly an influential and alternative approach that can be exploited for drug development against PTPs. Unlike active-site inhibitors, allosteric inhibitors exhibit a remarkable target-selectivity, drug-likeness, potency, and in vivo activity. Intriguingly, there has been a high interest in novel allosteric PTPs inhibitors within the last years. In this review, we focus on the recent advances of allosteric inhibitors that have been explored in drug discovery and have shown an excellent result in the development of PTPs-based therapeutics. A special emphasis is placed on the structure-activity relationship and molecular mechanistic studies illustrating applications in chemical biology and medicinal chemistry.
Collapse
Affiliation(s)
- Reham M Elhassan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| |
Collapse
|
9
|
Sánchez-Alonso P, Griera M, García-Marín J, Rodríguez-Puyol M, Alajarín R, Vaquero JJ, Rodríguez-Puyol D. Pyrrolo[1,2-a]quinoxal-5-inium salts and 4,5-dihydropyrrolo[1,2-a]quinoxalines: Synthesis, activity and computational docking for protein tyrosine phosphatase 1B. Bioorg Med Chem 2021; 44:116295. [PMID: 34246920 DOI: 10.1016/j.bmc.2021.116295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 11/17/2022]
Abstract
Protein tyrosine phosphatase (PTP1B) is an interesting therapeutical target for diabetes, obesity, heart disease and cancer. As such, inhibition of PTP1B using orally administered drugs is still being pursued by academia and pharmaceutical companies. The failure of catalytic-site inhibitors led to the focus in this field being switched to allosteric inhibitors. To date, the non-competitive inhibitors that have reached clinical trials target the site formed by the α3/α6/α7 tunnel or the site found in a disordered C-terminal non-catalytic segment. Herein, pyrrolo[1,2-a]quinoxal-5-inium salts and 4,5-dihydropyrrolo[1,2-a]quinoxalines are synthesized from pyrrolo[1,2-a]quinoxalines by alkylation and reduction, respectively. These compounds showed no toxicity in HepG2 cells and exhibited inhibitory activity against PTP1B, with inhibition percentages of between 37% and 53% at 1 μM and activities (IC50) of between 0.25 and 1.90 μM. The inhibitory activity against T-cell protein tyrosine phosphatase (TC-TPT) was also assayed, with 4,5-dihydropyrrolo[1,2-a]quinoxalines being found to be slightly more active and selective. Compounds from the two series behave as insulin mimetics since they exhibit enhancement of glucose uptake in C2C12 cells. Computational docking studies provide information about the putative binding mode for both series and the preference for the α3/α6/α7 allosteric tunnel.
Collapse
Affiliation(s)
- Patricia Sánchez-Alonso
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain
| | | | - Javier García-Marín
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain; Instituto de Investigación Química Andrés M. del Río (IQAR), Facultad de Farmacia, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain
| | - Manuel Rodríguez-Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain; Departamento de Biología de Sistemas, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; Fundación Renal Iñigo Álvarez de Toledo (FRIAT) y REDinREN del Instituto de Salud Carlos III, Madrid, Spain
| | - Ramón Alajarín
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain; Instituto de Investigación Química Andrés M. del Río (IQAR), Facultad de Farmacia, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain.
| | - Juan J Vaquero
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain; Instituto de Investigación Química Andrés M. del Río (IQAR), Facultad de Farmacia, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain
| | - Diego Rodríguez-Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain; Departamento de Biología de Sistemas, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; Fundación Renal Iñigo Álvarez de Toledo (FRIAT) y REDinREN del Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
10
|
Prediction of Pharmacokinetics Parameter and Molecular Docking Study of Antidiabetic Compounds from Syzygium polyanthum and Syzygium cumini. JURNAL KIMIA SAINS DAN APLIKASI 2020. [DOI: 10.14710/jksa.23.6.189-195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Syzygium polyanthum leaf extract and Syzygium cumini herbs extract have been reported to have antidiabetic activity. This study aimed to predict the molecular target of chemical constituents of S. polyanthum and S. cumini as well as study their interactions with various macromolecular targets of an antidiabetic agent. Molecular docking of all ligands was studied using the Autodock Vina program in PyRx, and the results are presented as binding affinity values (kcal/mol) of ligand against the protein. PyMOL is used to visualize the 3D molecular of docked conformation and ligand-protein interactions. The predicted pharmacokinetic parameters were obtained by SwissADME. Delphinidin-3-gentiobioside and isoquercitrin are predicted to have good interaction with DPP-4 and α-glucosidase, respectively. However, they are predicted to have poor absorption properties. Quercetin and kaempferol are predicted to have good interaction with PTP1B and glucokinase and showed good pharmacokinetic properties.
Collapse
|
11
|
Yuan X, Bu H, Zhou J, Yang CY, Zhang H. Recent Advances of SHP2 Inhibitors in Cancer Therapy: Current Development and Clinical Application. J Med Chem 2020; 63:11368-11396. [DOI: 10.1021/acs.jmedchem.0c00249] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xinrui Yuan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Hong Bu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| |
Collapse
|
12
|
Maheshwari N, Karthikeyan C, Bhadada SV, Verma AK, Sahi C, Moorthy NHN, Trivedi P. Design, synthesis and biological evaluation of some tetrazole acetamide derivatives as novel non-carboxylic PTP1B inhibitors. Bioorg Chem 2019; 92:103221. [DOI: 10.1016/j.bioorg.2019.103221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/05/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022]
|
13
|
Khan S, Bjij I, Soliman MES. Selective Covalent Inhibition of “Allosteric Cys121” Distort the Binding of PTP1B Enzyme: A Novel Therapeutic Approach for Cancer Treatment. Cell Biochem Biophys 2019; 77:203-211. [DOI: 10.1007/s12013-019-00882-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/09/2019] [Indexed: 02/05/2023]
|
14
|
Han RY, Ge Y, Zhang L, Wang QM. Design and Biological Evaluation of Novel Imidazolyl Flavonoids as Potent and Selective Protein Tyrosine Phosphatase Inhibitors. Med Chem 2019; 16:563-574. [PMID: 31208312 DOI: 10.2174/1573406415666190430125547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein tyrosine phosphatases 1B are considered to be a desirable validated target for therapeutic development of type II diabetes and obesity. METHODS A new series of imidazolyl flavonoids as potential protein tyrosine phosphatase inhibitors were synthesized and evaluated. RESULTS Bioactive results indicated that some synthesized compounds exhibited potent protein phosphatase 1B (PTP1B) inhibitory activities at the micromolar range. Especially, compound 8b showed the best inhibitory activity (IC50=1.0 µM) with 15-fold selectivity for PTP1B over the closely related T-cell protein tyrosine phosphatase (TCPTP). Cell viability assays indicated that 8b is cell permeable with lower cytotoxicity. Molecular modeling and dynamics studies revealed the reason for selectivity of PTP1B over TCPTP. Quantum chemical studies were carried out on these compounds to understand the structural features essential for activity. CONCLUSION Compound 8b should be a potential selective PTP1B inhibitor.
Collapse
Affiliation(s)
- Rong Y Han
- School of Pharmacy, Yancheng Teacher's University, Yancheng, Jiangsu 224051, China
| | - Yu Ge
- School of Pharmacy, Yancheng Teacher's University, Yancheng, Jiangsu 224051, China
| | - Ling Zhang
- School of Pharmacy, Yancheng Teacher's University, Yancheng, Jiangsu 224051, China
| | - Qing M Wang
- School of Pharmacy, Yancheng Teacher's University, Yancheng, Jiangsu 224051, China
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Identification of novel imidazole flavonoids as potent and selective inhibitors of protein tyrosine phosphatase. Bioorg Chem 2019; 88:102900. [PMID: 30991192 DOI: 10.1016/j.bioorg.2019.03.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/18/2019] [Accepted: 03/30/2019] [Indexed: 01/12/2023]
Abstract
A series of imidazole flavonoids as new type of protein tyrosine phosphatase inhibitors were synthesized and characterized. Most of them gave potent protein phosphatase 1B (PTP1B) inhibitory activities. Especially, compound 11a could effectively inhibit PTP1B with an IC50 value of 0.63 μM accompanied with high selectivity ratio (9.5-fold) over T-cell protein tyrosine phosphatase (TCPTP). This compound is cell permeable with relatively low cytotoxicity. The high binding affinity and selectivity was disclosed by molecular modeling and dynamics studies. The structural features essential for activity were confirmed by quantum chemical studies.
Collapse
|
17
|
Marsh-Armstrong B, Fajnzylber JM, Korntner S, Plaman BA, Bishop AC. The Allosteric Site on SHP2's Protein Tyrosine Phosphatase Domain is Targetable with Druglike Small Molecules. ACS OMEGA 2018; 3:15763-15770. [PMID: 30533581 PMCID: PMC6275946 DOI: 10.1021/acsomega.8b02200] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/23/2018] [Indexed: 06/09/2023]
Abstract
Difficulties in developing active-site-directed protein tyrosine phosphatase (PTP) inhibitors have led to the perception that PTPs are "undruggable", highlighting the need for new means to target pharmaceutically important PTPs allosterically. Recently, we characterized an allosteric-inhibition site on the PTP domain of Src-homology-2-domain-containing PTP 2 (SHP2), a key anticancer drug target. The central feature of SHP2's allosteric site is a nonconserved cysteine residue (C333) that can potentially be labeled with electrophilic compounds for selective SHP2 inhibition. Here, we describe the first directed discovery effort for C333-targeted allosteric SHP2 inhibitors. By screening a previously reported library of reversible, covalent inhibitors, we identified a lead compound, which was modified to yield an irreversible inhibitor (12), that inhibits SHP2 allosterically and selectively through interaction with C333. These findings provide a novel paradigm for allosteric-inhibitor discovery on SHP2, one that may help to circumvent the challenges inherent in targeting SHP2's active site.
Collapse
|
18
|
Zhang L, Ge Y, Song HM, Wang QM, Zhou CH. Design, synthesis of novel azolyl flavonoids and their protein tyrosine Phosphatase-1B inhibitory activities. Bioorg Chem 2018; 80:195-203. [DOI: 10.1016/j.bioorg.2018.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/30/2018] [Accepted: 06/03/2018] [Indexed: 12/15/2022]
|
19
|
Cysteine modifiers suggest an allosteric inhibitory site on the CAL PDZ domain. Biosci Rep 2018; 38:BSR20180231. [PMID: 29472314 PMCID: PMC6435542 DOI: 10.1042/bsr20180231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/17/2018] [Accepted: 02/22/2018] [Indexed: 01/28/2023] Open
Abstract
Protein-protein interactions have become attractive targets for both experimental and therapeutic interventions. The PSD-95/Dlg1/ZO-1 (PDZ) domain is found in a large family of eukaryotic scaffold proteins that plays important roles in intracellular trafficking and localization of many target proteins. Here, we seek inhibitors of the PDZ protein that facilitates post-endocytic degradation of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR): the CFTR-associated ligand (CAL). We develop and validate biochemical screens and identify methyl-3,4-dephostatin (MD) and its analog ethyl-3,4-dephostatin (ED) as CAL PDZ inhibitors. Depending on conditions, MD can bind either covalently or non-covalently. Crystallographic and NMR data confirm that MD attacks a pocket at a site distinct from the canonical peptide-binding groove, and suggests an allosteric connection between target residue Cys319 and the conserved Leu291 in the GLGI motif. MD and ED thus appear to represent the first examples of small-molecule allosteric regulation of PDZ:peptide affinity. Their mechanism of action may exploit the known conformational plasticity of the PDZ domains and suggests that allosteric modulation may represent a strategy for targeting of this family of protein-protein binding modules.
Collapse
|
20
|
Ruddraraju KV, Zhang ZY. Covalent inhibition of protein tyrosine phosphatases. MOLECULAR BIOSYSTEMS 2018; 13:1257-1279. [PMID: 28534914 DOI: 10.1039/c7mb00151g] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine residues on proteins serve as a ubiquitous mechanism for cellular signal transduction. Aberrant function of PTPs can lead to many human diseases, such as diabetes, obesity, cancer, and autoimmune diseases. As the number of disease relevant PTPs increases, there is urgency in developing highly potent inhibitors that are selective towards specific PTPs. Most current efforts have been devoted to the development of active site-directed and reversible inhibitors for PTPs. This review summarizes recent progress made in the field of covalent inhibitors to target PTPs. Here, we discuss the in vivo and in vitro inactivation of various PTPs by small molecule-containing electrophiles, such as Michael acceptors, α-halo ketones, epoxides, and isothiocyanates, etc. as well as oxidizing agents. We also suggest potential strategies to transform these electrophiles into isozyme selective covalent PTP inhibitors.
Collapse
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, IN 47907, USA.
| | | |
Collapse
|
21
|
Kumar AP, Nguyen MN, Verma C, Lukman S. Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites. Proteins 2018; 86:301-321. [PMID: 29235148 DOI: 10.1002/prot.25440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/16/2017] [Accepted: 12/10/2017] [Indexed: 12/11/2022]
Abstract
Catalytic proteins such as human protein tyrosine phosphatase 1B (PTP1B), with conserved and highly polar active sites, warrant the discovery of druggable nonactive sites, such as allosteric sites, and potentially, therapeutic small molecules that can bind to these sites. Catalyzing the dephosphorylation of numerous substrates, PTP1B is physiologically important in intracellular signal transduction pathways in diverse cell types and tissues. Aberrant PTP1B is associated with obesity, diabetes, cancers, and neurodegenerative disorders. Utilizing clustering methods (based on root mean square deviation, principal component analysis, nonnegative matrix factorization, and independent component analysis), we have examined multiple PTP1B structures. Using the resulting representative structures in different conformational states, we determined consensus clustroids and used them to identify both known and novel binding sites, some of which are potentially allosteric. We report several lead compounds that could potentially bind to the novel PTP1B binding sites and can be further optimized. Considering the possibility for drug repurposing, we discovered homologous binding sites in other proteins, with ligands that could potentially bind to the novel PTP1B binding sites.
Collapse
Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Minh N Nguyen
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| |
Collapse
|