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Bennett GM, Starczewski J, dela Cerna MVC. In silico identification of putative druggable pockets in PRL3, a significant oncology target. Biochem Biophys Rep 2024; 39:101767. [PMID: 39050014 PMCID: PMC11267023 DOI: 10.1016/j.bbrep.2024.101767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Protein tyrosine phosphatases (PTP) have emerged as targets in diseases characterized by aberrant phosphorylations such as cancers. The activity of the phosphatase of regenerating liver 3, PRL3, has been linked to several oncogenic and metastatic pathways, particularly in breast, ovarian, colorectal, and blood cancers. Development of small molecules that directly target PRL3, however, has been challenging. This is partly due to the lack of structural information on how PRL3 interacts with its inhibitors. Here, computational methods are used to bridge this gap by evaluating the druggability of PRL3. In particular, web-based pocket prediction tools, DoGSite3 and FTMap, were used to identify binding pockets using structures of PRL3 currently available in the Protein Data Bank. Druggability assessment by molecular dynamics simulations with probes was also performed to validate these results and to predict the strength of binding in the identified pockets. While several druggable pockets were identified, those in the closed conformation show more promise given their volume and depth. These two pockets flank the active site loops and roughly correspond to pockets predicted by molecular docking in previous papers. Notably, druggability simulations predict the possibility of low nanomolar affinity inhibitors in these sites implying the potential to identify highly potent small molecule inhibitors for PRL3. Putative pockets identified here can be leveraged for high-throughput virtual screening to further accelerate the drug discovery against PRL3 and development of PRL3-directed therapeutics.
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Affiliation(s)
- Grace M. Bennett
- Department of Biochemistry, Chemistry, and Physics, Georgia Southern University, Savannah, GA, 31419, USA
| | - Julia Starczewski
- Department of Biochemistry, Chemistry, and Physics, Georgia Southern University, Savannah, GA, 31419, USA
| | - Mark Vincent C. dela Cerna
- Department of Biochemistry, Chemistry, and Physics, Georgia Southern University, Savannah, GA, 31419, USA
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2
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Yang L, Zhao H, Yuan F, Chen M, Ma N, Yin Z, Liu H, Guo Y. Computational study on the binding mechanism of allosteric drug TNO155 inhibiting SHP2 E76A. Mol Divers 2024:10.1007/s11030-024-10881-1. [PMID: 38807000 DOI: 10.1007/s11030-024-10881-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
E76A mutations of SHP2 have been reported to associate with genetic developmental diseases and cancers, and TNO155 is one of the effective inhibitors targeted to the allosteric site 1, which has already entered the clinical stage. However, the detailed binding mechanism between them still needs further clarification at micro-atomic level. In this study, the binding mechanism of TNO155 inhibiting SHP2E76A and the superiorities of TNO155 at binding affinity and dynamic interactive behavior with SHP2E76A were probed utilizing a series of computational drug design technologies. The results show that SHP2E76A forms tighter interaction with TNO155 compared to SHP099. SHP2E76A-TNO155 exhibits the largest electrostatic interaction among all complex systems, which can be manifested by the strong hydrogen bond interactions formed by two electrically charged residues, Arg111 and Glu250. Notably, in SHP2E76A-TNO155 system, Asp489 makes an additional substantial beneficial contribution. The E76A mutation brings stronger residue positive correlation and a larger conformation fluctuation between N-CH2 and PTP domains, resulting in tighter binding between TNO155 and SHP2E76A. This study offers valuable insights for the further design and development of novel SHP2E76A allosteric inhibitors.
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Affiliation(s)
- Longhua Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Huijian Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fanru Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mengguo Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Nannan Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhili Yin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Henan Province for Drug Quality and Evaluation, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, 450001, China
| | - Yong Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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3
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Bourlon MT, Urbina-Ramirez S, Verduzco-Aguirre HC, Mora-Pineda M, Velazquez HE, Leon-Rodriguez E, Atisha-Fregoso Y, De Anda-Gonzalez MG. Differences in the expression of the phosphatase PTP-1B in patients with localized prostate cancer with and without adverse pathological features. Front Oncol 2024; 14:1334845. [PMID: 38706600 PMCID: PMC11066170 DOI: 10.3389/fonc.2024.1334845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Patients with adverse pathological features (APF) at radical prostatectomy (RP) for prostate cancer (PC) are candidates for adjuvant treatment. Clinicians lack reliable markers to predict these APF preoperatively. Protein tyrosine phosphatase 1B (PTP-1B) is involved in migration and invasion of PC, and its expression could predict presence of APF. Our aim was to compare PTP-1B expression in patients with and without APF, and to explore PTP-1B expression as an independent prognostic factor. Methods Tissue microarrays (TMAs) were constructed using RP archival specimens for immunohistochemical staining of PTP-1B; expression was reported with a standardized score (0-9). We compared median PTP-1B score between cases with and without APF. We constructed two logistic regression models, one to identify the independence of PTP-1B score from biologically associated variables (metformin use and type 2 diabetes mellitus [T2DM]) and the second to seek independence of known risk factors (Gleason score and prostate specific antigen [PSA]). Results A total of 73 specimens were suitable for TMA construction. Forty-four (60%) patients had APF. The median PTP-1B score was higher in those with APF: 8 (5-9) vs 5 (3-8) (p=0.026). In the logistic regression model including T2DM and metformin use, the PTP-1B score maintained statistical significance (OR 1.21, 95% CI 1.01-1.45, p=0.037). In the model including PSA and Gleason score; the PTP-1B score showed no independence (OR 1.68, 95% CI 0.97-1.41, p=0.11). The area under the curve to predict APF for the PTP-1B score was 0.65 (95% CI 0.52-0.78, p=0.03), for PSA+Gleason 0.71 (95% CI 0.59-0.82, p=0.03), and for PSA+Gleason+PTP-1B score 0.73 (95% CI 0.61-0.84, p=0.001). Discussion Patients with APF after RP have a higher expression of PTP-1B than those without APF, even after adjusting for T2DM and metformin exposure. PTP-1B has a good accuracy for predicting APF but does not add to known prognostic factors.
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Affiliation(s)
- Maria T. Bourlon
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
- Universidad Panamericana, Escuela de Medicina, Mexico City, Mexico
| | - Shaddai Urbina-Ramirez
- Department of Pathology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Haydee C. Verduzco-Aguirre
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Mauricio Mora-Pineda
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Hugo E. Velazquez
- Instituto Nacional de Cardiología “Ignacio Chavez”, Radiology Department, Mexico City, Mexico
| | - Eucario Leon-Rodriguez
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Yemil Atisha-Fregoso
- Instituto Tecnológico de Estudios Superiores de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - María G. De Anda-Gonzalez
- Department of Pathology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
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Zinovjev K, Guénon P, Ramos-Guzmán CA, Ruiz-Pernía JJ, Laage D, Tuñón I. Activation and friction in enzymatic loop opening and closing dynamics. Nat Commun 2024; 15:2490. [PMID: 38509080 PMCID: PMC10955111 DOI: 10.1038/s41467-024-46723-9] [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: 08/02/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechanism and rate-limiting step for WPD-loop dynamics in the PTP1B enzyme. While protein conformational dynamics is often represented as diffusive motion hindered by solvent viscosity and internal friction, we demonstrate that loop opening and closing is activated. It is governed by torsional rearrangement around a single loop peptide group and by significant friction caused by backbone adjustments, which can dynamically trap the loop. Considering both torsional barrier and time-dependent friction, our calculated rate constants exhibit very good agreement with experimental measurements, reproducing the change in loop opening kinetics between proteins. Furthermore, we demonstrate the applicability of our results to other enzymatic loops, including the M20 DHFR loop, thereby offering prospects for loop engineering potentially leading to enhanced designs.
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Affiliation(s)
- Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia, 46100, Burjasot, Spain
| | - Paul Guénon
- Departamento de Química Física, Universidad de Valencia, 46100, Burjasot, Spain
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Carlos A Ramos-Guzmán
- Departamento de Química Física, Universidad de Valencia, 46100, Burjasot, Spain
- Instituto de Materiales Avanzados, Universidad Jaume I, 12071, Castelló, Spain
| | | | - Damien Laage
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, 46100, Burjasot, Spain.
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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Bhavana, Kohal R, Kumari P, Das Gupta G, Kumar Verma S. Druggable targets of protein tyrosine phosphatase Family, viz. PTP1B, SHP2, Cdc25, and LMW-PTP: Current scenario on medicinal Attributes, and SAR insights. Bioorg Chem 2024; 144:107121. [PMID: 38237392 DOI: 10.1016/j.bioorg.2024.107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Protein tyrosine phosphatases (PTPs) are the class of dephosphorylation enzymes that catalyze the removal of phosphate groups from tyrosine residues on proteins responsible for various cellular processes. Any disbalance in signal pathways mediated by PTPs leads to various disease conditions like diabetes, obesity, cancers, and autoimmune disorders. Amongst the PTP superfamily, PTP1B, SHP2, Cdc25, and LMW-PTP have been prioritized as druggable targets for developing medicinal agents. PTP1B is an intracellular PTP enzyme that downregulates insulin and leptin signaling pathways and is involved in insulin resistance and glucose homeostasis. SHP2 is involved in the RAS-MAPK pathway and T cell immunity. Cdk-cyclin complex activation occurs by Cdc25-PTPs involved in cell cycle regulation. LMW-PTPs are involved in PDGF/PDGFR, Eph/ephrin, and insulin signaling pathways, resulting in certain diseases like diabetes mellitus, obesity, and cancer. The signaling cascades of PTP1B, SHP2, Cdc25, and LMW-PTPs have been described to rationalize their medicinal importance in the pathophysiology of diabetes, obesity, and cancer. Their binding sites have been explored to overcome the hurdles in discovering target selective molecules with optimum potency. Recent developments in the synthetic molecules bearing heterocyclic moieties against these targets have been explored to gain insight into structural features. The elaborated SAR investigation revealed the effect of substituents on the potency and target selectivity, which can be implicated in the further discovery of newer medicinal agents targeting the druggable members of the PTP superfamily.
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Affiliation(s)
- Bhavana
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Rupali Kohal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Preety Kumari
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Ghanshyam Das Gupta
- Department of Pharmaceutics, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India.
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Xu X, Wang L, Zhang K, Zhang Y, Fan G. Managing metabolic diseases: The roles and therapeutic prospects of herb-derived polysaccharides. Biomed Pharmacother 2023; 161:114538. [PMID: 36931026 DOI: 10.1016/j.biopha.2023.114538] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/25/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Metabolic diseases have become a public health problem worldwide. Effective, novel and natural therapies are urgently needed to treat metabolic diseases. As natural bioactive compounds, polysaccharides have many physiological and medicinal properties. Recently, herb-derived polysaccharides have shown beneficial effects in the treatment of metabolic diseases, but the underlying mechanisms remain unclear. This review comprehensively summarizes the pharmacological progress and clinical evidence of herb-derived polysaccharides in the treatment of three metabolic diseases, namely type 2 diabetes mellitus, nonalcoholic fatty liver disease and obesity, and more importantly, discusses the molecular mechanism involved. Existing evidence has proved that herb-derived polysaccharides can maintain glucose homeostasis, promote insulin secretion, improve insulin resistance, reduce weight gain and hepatic steatosis, inhibit lipogenesis, alleviate oxidative stress and inflammation, and improve gut microbiota disorders in rodents with metabolic diseases. Notably, so far, human clinical trials of herb-derived polysaccharides for these three metabolic diseases remain rare. All in all, herb-derived polysaccharides may have good potential as drug candidates for the prevention and management of metabolic diseases. More high-quality clinical trials are needed to further validate its effectiveness and safety in human subjects.
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Affiliation(s)
- Xinmei Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lijie Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kun Zhang
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yi Zhang
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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7
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Bourebaba L, Serwotka-Suszczak A, Pielok A, Sikora M, Mularczyk M, Marycz K. The PTP1B inhibitor MSI-1436 ameliorates liver insulin sensitivity by modulating autophagy, ER stress and systemic inflammation in Equine metabolic syndrome affected horses. Front Endocrinol (Lausanne) 2023; 14:1149610. [PMID: 37020593 PMCID: PMC10067883 DOI: 10.3389/fendo.2023.1149610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Equine metabolic syndrome (EMS) is a multifactorial pathology gathering insulin resistance, low-grade inflammation and past or chronic laminitis. Among the several molecular mechanisms underlying EMS pathogenesis, increased negative insulin signalling regulation mediated by protein tyrosine phosphatase 1 B (PTP1B) has emerged as a critical axis in the development of liver insulin resistance and general metabolic distress associated to increased ER stress, inflammation and disrupted autophagy. Thus, the use of PTP1B selective inhibitors such as MSI-1436 might be considered as a golden therapeutic tool for the proper management of EMS and associated conditions. Therefore, the present investigation aimed at verifying the clinical efficacy of MSI-1436 systemic administration on liver metabolic balance, insulin sensitivity and inflammatory status in EMS affected horses. Moreover, the impact of MSI-1436 treatment on liver autophagy machinery and associated ER stress in liver tissue has been analysed. METHODS Liver explants isolated from healthy and EMS horses have been treated with MSI-1436 prior to gene and protein expression analysis of main markers mediating ER stress, mitophagy and autophagy. Furthermore, EMS horses have been intravenously treated with a single dose of MSI-1436, and evaluated for their metabolic and inflammatory status. RESULTS Clinical application of MSI-1436 to EMS horses restored proper adiponectin levels and attenuated the typical hyperinsulinemia and hyperglycemia. Moreover, administration of MSI-1436 further reduced the circulating levels of key pro-inflammatory mediators including IL-1β, TNF-α and TGF-β and triggered the Tregs cells activation. At the molecular level, PTP1B inhibition resulted in a noticeable mitigation of liver ER stress, improvement of mitochondrial dynamics and consequently, a regulation of autophagic response. Similarly, short-term ex vivo treatment of EMS liver explants with trodusquemine (MSI-1436) substantially enhanced autophagy by upregulating the levels of HSC70 and Beclin-1 at both mRNA and protein level. Moreover, the PTP1B inhibitor potentiated mitophagy and associated expression of MFN2 and PINK1. Interestingly, inhibition of PTP1B resulted in potent attenuation of ER stress key mediators' expression namely, CHOP, ATF6, HSPA5 and XBP1. CONCLUSION Presented findings shed for the first time promising new insights in the development of an MSI-1436-based therapy for proper equine metabolic syndrome intervention and may additionally find potential translational application to human metabolic syndrome treatment.
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Affiliation(s)
- Lynda Bourebaba
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- International Institute of Translational Medicine, Wisznia Mała, Poland
| | - Anna Serwotka-Suszczak
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Ariadna Pielok
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Mateusz Sikora
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Malwina Mularczyk
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- International Institute of Translational Medicine, Wisznia Mała, Poland
| | - Krzysztof Marycz
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- *Correspondence: Krzysztof Marycz,
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Sharma S, Ebrahim A, Keedy DA. Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B. Acta Crystallogr F Struct Biol Commun 2023; 79:23-30. [PMID: 36598353 PMCID: PMC9813971 DOI: 10.1107/s2053230x22011645] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022] Open
Abstract
Room-temperature X-ray crystallography provides unique insights into protein conformational heterogeneity, but obtaining sufficiently large protein crystals is a common hurdle. Serial synchrotron crystallography (SSX) helps to address this hurdle by allowing the use of many medium- to small-sized crystals. Here, a recently introduced serial sample-support chip system has been used to obtain the first SSX structure of a human phosphatase, specifically protein tyrosine phosphatase 1B (PTP1B) in the unliganded (apo) state. In previous apo room-temperature structures, the active site and allosteric sites adopted alternate conformations, including open and closed conformations of the active-site WPD loop and of a distal allosteric site. By contrast, in our SSX structure the active site is best fitted with a single conformation, but the distal allosteric site is best fitted with alternate conformations. This observation argues for additional nuance in interpreting the nature of allosteric coupling in this protein. Overall, our results illustrate the promise of serial methods for room-temperature crystallography, as well as future avant-garde crystallography experiments, for PTP1B and other proteins.
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Affiliation(s)
- Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- PhD Program in Biology, CUNY Graduate Center, New York, NY 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
- PhD Programs in Biochemistry, Biology and Chemistry, CUNY Graduate Center, New York, NY 10016, USA
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Wiśniewska K, Siatkowska M, Komorowski P, Napieralska K, Kasperkiewicz K, Surmiak-Stalmach K, Wilczek G. Effects of chronic exposure to cadmium and copper on the proteome profile of hemolymph in false widow spider Steatoda grossa (Theridiidae). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114448. [PMID: 38321667 DOI: 10.1016/j.ecoenv.2022.114448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/28/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2024]
Abstract
The aim of this study was to evaluate the quantitative and qualitative changes in the proteome of the hemolymph of female Steatoda grossa spiders (Theridiidae) that were chronically exposed to cadmium and copper in food and were additionally immunostimulated (phorbol 12-myristate 13-acetate (PMA); bacterial suspensions: Staphylococcus aureus (G+), Pseudomonas fluorescens (G-). It was found that the expression of nearly 90 proteins was altered in cadmium-intoxicated spiders and more than 60 in copper-exposed individuals. Regardless of the type of metal used, these proteins were mainly overexpressed in the hemolymph of the exposed spiders. On the other hand, immunostimulation did not significantly change the number of proteins with altered expression in metal-intoxicated individuals. Hemocyanin (Hc) was found to be the most abundant of the proteins identified with altered expression. In copper-intoxicated spiders, immunostimulation increased the expression of A-, E-, F-, and G-chain-containing proteins, while in the case of cadmium-intoxicates spiders, it decreased the expression of E- and A-chain-containing Hc and increased the expression of G-chain-containing Hc. Regardless of the type of metal and immunostimulant used, there was an increase in the expression of actin. In addition, cadmium increased the expression of cullin, vimentin, and ceruloplasmin. The changes observed in the expression of hemolymph proteins indicate their protective function in S. grossa (Theridiidae) spiders under conditions of metal exposure.
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Affiliation(s)
- Kamila Wiśniewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Małgorzata Siatkowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland; Laboratory of Molecular and Nanostructural Biophysics, Bionanopark Ltd. Dubois 114/116, 93-465 Łódź, Poland
| | - Piotr Komorowski
- Laboratory of Molecular and Nanostructural Biophysics, Bionanopark Ltd. Dubois 114/116, 93-465 Łódź, Poland; Department of Biophysics, Institute of Materials Science, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Kinga Napieralska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland; Laboratory of Molecular and Nanostructural Biophysics, Bionanopark Ltd. Dubois 114/116, 93-465 Łódź, Poland
| | - Katarzyna Kasperkiewicz
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Kinga Surmiak-Stalmach
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Grażyna Wilczek
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland.
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Bacterial Protein Tyrosine Phosphatases as Possible Targets for Antimicrobial Therapies in Response to Antibiotic Resistance. Antioxidants (Basel) 2022; 11:antiox11122397. [PMID: 36552605 PMCID: PMC9774629 DOI: 10.3390/antiox11122397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The review is focused on the bacterial protein tyrosine phosphatases (PTPs) utilized by bacteria as virulence factors necessary for pathogenicity. The inhibition of bacterial PTPs could contribute to the arrest of the bacterial infection process. This mechanism could be utilized in the design of antimicrobial therapy as adjuvants to antibiotics. The review summaries knowledge on pathogenic bacterial protein tyrosine phosphatases (PTPs) involved in infection process, such as: PTPA and PTPB from Staphylococcus aureus and Mycobacterium tuberculosis; SptP from Salmonella typhimurium; YopH from Yersinia sp. and TbpA from Pseudomonas aeruginosa. The review focuses also on the potential inhibitory compounds of bacterial virulence factors and inhibitory mechanisms such as the reversible oxidation of tyrosine phosphatases.
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11
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Yarnall MT, Kim SH, Korntner S, Bishop AC. Destabilization of the SHP2 and SHP1 protein tyrosine phosphatase domains by a non-conserved "backdoor" cysteine. Biochem Biophys Rep 2022; 32:101370. [PMID: 36275931 PMCID: PMC9578986 DOI: 10.1016/j.bbrep.2022.101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are critical regulators of cellular signal transduction that catalyze the hydrolytic dephosphorylation of phosphotyrosine in substrate proteins. Among several conserved features in classical PTP domains are an active-site cysteine residue that is necessary for catalysis and a "backdoor" cysteine residue that can serve to protect the active-site cysteine from irreversible oxidation. Curiously, two biologically important phosphatases, Src homology domain-containing PTPs 2 and 1 (SHP2 and SHP1), each contain an additional backdoor cysteine residue at a position of the PTP domain that is occupied by proline in almost all other classical PTPs (position 333 in human SHP2 numbering). Here we show that the presence of cysteine 333 significantly destabilizes the fold of the PTP domains in the SHPs. We find that replacement of cysteine 333 with proline confers increased thermal stability on the SHP2 and SHP1 PTP domains, as measured by temperature-dependent activity assays and differential scanning fluorimetry. Conversely, we show that substantial destabilization of the PTP-domain fold is conferred by introduction of a non-natural cysteine residue in a non-SHP PTP that contains proline at the 333 position. It has previously been suggested that the extra backdoor cysteine of the SHP PTPs may work in tandem with the conserved backdoor cysteine to provide protection from irreversible oxidative enzyme inactivation. If so, our current results suggest that, during the course of mammalian evolution, the SHP proteins have developed extra protection from oxidation at the cost of the thermal instability that is conferred by the presence of their PTP domains' second backdoor cysteine.
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Affiliation(s)
| | - Sean H. Kim
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
| | - Samuel Korntner
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
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12
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Behl T, Gupta A, Sehgal A, Albarrati A, Albratty M, Meraya AM, Najmi A, Bhatia S, Bungau S. Exploring protein tyrosine phosphatases (PTP) and PTP-1B inhibitors in management of diabetes mellitus. Biomed Pharmacother 2022; 153:113405. [DOI: 10.1016/j.biopha.2022.113405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/02/2022] Open
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13
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Yao FH, Liang X, Lu XH, Cheng X, Luo LX, Qi SH. Pyrrospirones K-Q, Decahydrofluorene-Class Alkaloids from the Marine-Derived Fungus Penicillium sp. SCSIO 41512. JOURNAL OF NATURAL PRODUCTS 2022; 85:2071-2081. [PMID: 35930265 DOI: 10.1021/acs.jnatprod.2c00473] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Seven new decahydrofluorene-class alkaloids, pyrrospirones K-Q (1-7), together with six known analogues (8-13) were isolated from the marine-derived fungal strain Penicillium sp. SCSIO 41512. Their structures were determined by extensive spectroscopic analysis, and their absolute configurations were established by single-crystal X-ray diffraction analysis and quantum chemical calculations of electronic circular dichroism spectra. Compounds 1 and 3 possess a novel decahydrofluorene-class alkaloid skeleton with a 6/5/6/8/5/6/13 and a 6/5/6/5/6/13 polycyclic system, respectively. Biologically, 13 displayed significant inhibitory activity against protein tyrosine phosphatases CD45, TCPTP, SHP1, and PTP1B with IC50 values of 8.1-17.8 μM, and 1, 2, 5, 8-10, 12, and 13 showed antibacterial activity against six pathogens. Their structure-activity relationship is also discussed.
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Affiliation(s)
- Fei-Hua Yao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Liang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, Guangdong, China
| | - Xin-Hua Lu
- New Drug Research Development Center of North China Pharmaceutical Group Corporation, Shijiazhuang, 0521655, China
| | - Xia Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lian-Xiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Shu-Hua Qi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
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14
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Elgamal HA, Mohamed SA, Farghali AA, Hassan AME. PEG@ Carbon Nanotubes Composite as an Effective Nanocarrier of Ixazomib for Myeloma Cancer Therapy. NANOSCALE RESEARCH LETTERS 2022; 17:72. [PMID: 35930196 PMCID: PMC9356125 DOI: 10.1186/s11671-022-03707-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
In this work, the preparation of a PEG@ multi-walled carbon nanotubes (MWCNTs) composite has shown a great potential effect in tumor therapy using graphite powder at room temperature. PEGylated MWCNTs were created and used as a carrier for targeting the antineoplastic drug Ixazomib to myeloma cancer cells (abnormal plasma cells). Ixazomib (MLN2238) was covalently encapsulated into functionalized carbon nanotubes modified with polyethylene glycol (PEG 600) to obtain MWCNTs-PEG-MLN2238. The Ixazomib@ MWCNTs-PEG composite shows promising results as an effective nanocarrier and using a small amount of MWCNTs-PEG-Ixazomib that has a low toxicity compared with that of Ixazomib alone. A multifunctional MWCNTs-PEG-Ixazomib composite is used to test biological effects on multiple myeloma cell lines RPMI 8226 using the MTT assay to enhance treatment efficiency. The cytotoxicity of free Ixazomib citrate (69% cell viability of RPMI8226 cells) was higher than that of MWCNTs-PEG-Ixazomib (91% cell viability) at the same maximum concentration of Ixazomib citrate (50 µg/ml). In this work, we performed a study of preparation of MWCNTs with an acceptable Ixazomib loading efficiency and determination of the drug systemic toxicity for the first time. In this study, the preparation of MWCNTs with acceptable Ixazomib loading efficiency and determination of the drug systemic toxicity was performed for the first time. The MTT assay results show decreasing the toxicity of Ixazomib after loading with the MWCNTs-PEG composite. The MWCNTs-PEG @ Ixazomib show promising results as an effective carrier of Ixazomib and lead to a decrease in the cost of using Ixazomib.
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Affiliation(s)
- Hanady A. Elgamal
- Material Science and Nanotechnology Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, 62511 Egypt
- National Organization of Drug Control and Research, Dokki, Egypt
| | | | - Ahmed A. Farghali
- Material Science and Nanotechnology Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, 62511 Egypt
| | - Abeer M. E. Hassan
- Analytical Chemistry Department, Faculty of Pharmacy, October 6 University, Giza, Egypt
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15
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Jassim BA, Lin J, Zhang ZY. PTPN22: Structure, Function, and Developments in Inhibitor Discovery with Applications for Immunotherapy. Expert Opin Drug Discov 2022; 17:825-837. [PMID: 35637605 PMCID: PMC9378720 DOI: 10.1080/17460441.2022.2084607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION While immunotherapy strategies such as immune checkpoint inhibition and adoptive T cell therapy have become commonplace in cancer therapy, they suffer from limitations, including lack of patient response and toxicity. To wield the maximum potential of the immune system, cancer immunotherapy must integrate novel targets and therapeutic strategies with potential to augment clinical efficacy of currently utilized immunotherapies. PTPN22, a member of the protein tyrosine phosphatase (PTP) superfamily that downregulates T cell signaling and proliferation, has recently emerged as a systemically druggable and novel immunotherapy target. AREAS COVERED This review describes the basics of PTPN22 structure and function and provides comprehensive insight into recent advances in small molecule PTPN22 inhibitor development and the immense potential of PTPN22 inhibition to synergize with current immunotherapies. EXPERT OPINION It is apparent that small molecule PTPN22 inhibitors have enormous potential to augment efficacy of current immunotherapy strategies such as checkpoint inhibition and adoptive cell transfer. Nevertheless, several constraints must be overcome before these inhibitors can be applied as useful therapeutics, namely selectivity, potency, and in vivo efficacy.
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Affiliation(s)
- Brenson A Jassim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, West Lafayette
| | - Jianping Lin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, West Lafayette
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, West Lafayette
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16
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Ghemrawi R, Khair M, Hasan S, Aldulaymi R, AlNeyadi SS, Atatreh N, Ghattas MA. The Discovery of Potent SHP2 Inhibitors with Anti-Proliferative Activity in Breast Cancer Cell Lines. Int J Mol Sci 2022; 23:ijms23084468. [PMID: 35457286 PMCID: PMC9030381 DOI: 10.3390/ijms23084468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/17/2022] [Indexed: 02/04/2023] Open
Abstract
Despite available treatments, breast cancer is the leading cause of cancer-related death. Knowing that the tyrosine phosphatase SHP2 is a regulator in tumorigenesis, developing inhibitors of SHP2 in breast cells is crucial. Our study investigated the effects of new compounds, purchased from NSC, on the phosphatase activity of SHP2 and the modulation of breast cancer cell lines’ proliferation and viability. A combined ligand-based and structure-based virtual screening protocol was validated, then performed, against SHP2 active site. Top ranked compounds were tested via SHP2 enzymatic assay, followed by measuring IC50 values. Subsequently, hits were tested for their anti-breast cancer viability and proliferative activity. Our experiments identified three compounds 13030, 24198, and 57774 as SHP2 inhibitors, with IC50 values in micromolar levels and considerable selectivity over the analogous enzyme SHP1. Long MD simulations of 500 ns showed a very promising binding mode in the SHP2 catalytic pocket. Furthermore, these compounds significantly reduced MCF-7 breast cancer cells’ proliferation and viability. Interestingly, two of our hits can have acridine or phenoxazine cyclic system known to intercalate in ds DNA. Therefore, our novel approach led to the discovery of SHP2 inhibitors, which could act as a starting point in the future for clinically useful anticancer agents.
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Affiliation(s)
- Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates; (R.G.); (S.H.)
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates;
| | - Mostafa Khair
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates;
| | - Shaima Hasan
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates; (R.G.); (S.H.)
| | - Raghad Aldulaymi
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates;
| | - Shaikha S. AlNeyadi
- Department of Chemistry, College of Science, UAE University Al-Ain, Abu Dhabi 15551, United Arab Emirates;
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates; (R.G.); (S.H.)
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates;
- Correspondence: (N.A.); (M.A.G.)
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, United Arab Emirates; (R.G.); (S.H.)
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates;
- Correspondence: (N.A.); (M.A.G.)
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17
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A selective PPM1A inhibitor activates autophagy to restrict the survival of Mycobacterium tuberculosis. Cell Chem Biol 2022; 29:1126-1139.e12. [PMID: 35320734 DOI: 10.1016/j.chembiol.2022.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/01/2022] [Accepted: 03/03/2022] [Indexed: 12/19/2022]
Abstract
Metal-dependent protein phosphatases (PPMs) have essential roles in a variety of cellular processes, including inflammation, proliferation, differentiation, and stress responses, which are intensively investigated in cancer and metabolic diseases. Targeting PPMs to modulate host immunity in response to pathogens is an ambitious proposition. The feasibility of such a strategy is unproven because development of inhibitors against PPMs is challenging and suffers from poor selectivity. Combining a biomimetic modularization strategy with function-oriented synthesis, we design, synthesize and screen more than 500 pseudo-natural products, resulting in the discovery of a potent, selective, and non-cytotoxic small molecule inhibitor for PPM1A, SMIP-30. Inhibition of PPM1A with SMIP-30 or its genetic ablation (ΔPPM1A) activated autophagy through a mechanism dependent on phosphorylation of p62-SQSTM1, which restricted the intracellular survival of Mycobacterium tuberculosis in macrophages and in the lungs of infected mice. SMIP-30 provides proof of concept that PPMs are druggable and promising targets for the development of host-directed therapies against tuberculosis.
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18
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Yang XT, Li TZ, Geng CA, Liu P, Chen JJ. Synthesis and biological evaluation of (20 S,24 R)-epoxy-dammarane-3β,12β,25-triol derivatives as α-glucosidase and PTP1B inhibitors. Med Chem Res 2022; 31:350-367. [PMID: 35035203 PMCID: PMC8749348 DOI: 10.1007/s00044-021-02836-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022]
Abstract
The dammarane triterpenoid (20S,24R)-epoxy-dammarane-3β,12β,25-triol obtained from Cyclocarya paliurus in our previous study showed inhibitory activity on α-glucosidase in vitro with an inhibitory ratio of 32.2% at the concentration of 200 μM. In order to reveal the structure-activity relationships (SARs) and get more active compounds, 42 derivatives of (20S,24R)-epoxy-dammarane-3β,12β,25-triol were synthesized by chemical modification on the hydroxyls (C-3 and C-12), rings A and E, and assayed for their α-glucosidase and PTP1B inhibitory activities. Two compounds (8, 26) increased activity against α-glucosidase, and four compounds (8, 15, 26, 42) significantly inhibited PTP1B. It was noted that compounds 8 and 26 could inhibit both α-glucosidase and PTP1B as dual-target inhibitors with IC50 values of 489.8, 467.7 μM (α-glucosidase) and 319.7, 269.1 μM (PTP1B). Compound 26 was revealed to be a mix-type inhibitor on α-glucosidase and a noncompetitive-type inhibitor on PTP1B based on enzyme kinetic study. Furthermore, compound 42 could selectively inhibited PTP1B as a mix-type inhibitor with IC50 value of 134.9 μM, which was 2.5-fold higher than the positive control, suramin sodium (IC50 339.0 μM), but not inhibit α-glucosidase. ![]()
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Affiliation(s)
- Xiao-Tong Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences; Yunnan Key Laboratory of Natural Medicinal Chemistry, 650201 Kunming, People's Republic of China
| | - Tian-Ze Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences; Yunnan Key Laboratory of Natural Medicinal Chemistry, 650201 Kunming, People's Republic of China
| | - Chang-An Geng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences; Yunnan Key Laboratory of Natural Medicinal Chemistry, 650201 Kunming, People's Republic of China
| | - Pei Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences; Yunnan Key Laboratory of Natural Medicinal Chemistry, 650201 Kunming, People's Republic of China
| | - Ji-Jun Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences; Yunnan Key Laboratory of Natural Medicinal Chemistry, 650201 Kunming, People's Republic of China.,University of Chinese Academy of Sciences, 100049 Beijing, People's Republic of China
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19
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Huang ZH, Liang X, Li CJ, Gu Q, Ma X, Qi SH. Talaromynoids A-I, Highly Oxygenated Meroterpenoids from the Marine-Derived Fungus Talaromyces purpureogenus SCSIO 41517 and Their Lipid Accumulation Inhibitory Activities. JOURNAL OF NATURAL PRODUCTS 2021; 84:2727-2737. [PMID: 34596414 DOI: 10.1021/acs.jnatprod.1c00681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nine new highly oxygenated 3,5-dimethylorsellinic acid-derived meroterpenoids, talaromynoids A-I (1-9), were isolated from the marine-derived fungus Talaromyces purpureogenus SCSIO 41517. Their structures including absolute configurations were elucidated by HRMS, NMR, single-crystal X-ray diffraction analysis, and electronic circular dichroism calculations. Compounds 1 and 7-9 possessed unprecedented 5/7/6/5/6/6, 6/7/6/6/6/5, 6/7/6/5/6/5/4, and 7/6/5/6/5/4 polycyclic systems, respectively. Biologically, compound 5 showed selective inhibitory activity against phosphatase CDC25B with an IC50 value of 13 μM. Moreover, 7-9 and 12 exhibited the activity of reducing triglyceride in 3T3-L1 adipocytes in a dosage-dependent manner.
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Affiliation(s)
- Zhong-Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiao Liang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Chan-Juan Li
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xuan Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Shu-Hua Qi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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20
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Wu J, Zhang H, Zhao G, Wang R. Allosteric Inhibitors of SHP2: An Updated Patent Review (2015-2020). Curr Med Chem 2021; 28:3825-3842. [PMID: 32988341 DOI: 10.2174/1568011817666200928114851] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/22/2022]
Abstract
Srchomology-2-domain-containing PTP 2 (SHP2) is a nonreceptor phosphatase encoded by the PTPN11 gene. Over expression of SHP2 is associated with various human diseases, such as Noonan syndrome, LEOPARD syndrome, and cancers. To overcome the shortcomings of existing orthosteric inhibitors, novel inhibitors targeting the allosteric site of SHP2 with high selectivity and low toxicity are under development. This paper reviews allosteric inhibitors of SHP2 published in patents from 2015 to 2020. The molecules are classified according to the chemical structure of the central core. SHP2 has long been considered as an 'undruggable' protein. Fortunately, a critical breakthrough was made by researchers from Novartis AG Ltd., who identified SHP099 as a highly potent, selective, soluble, and orally bioavailable SHP2 allosteric inhibitor. Currently, there are several allosteric inhibitors of SHP2 in clinical development. However, drug resistance is still a major challenge. The combination of SHP2 allosteric inhibitors and immunotherapy drugs or molecular targeted drugs is emerging as a promising therapeutic strategy against drug resistance.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, No. 22, Qixiangtai Road, Heping District, Tianjin 300070, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Guilong Zhao
- The Institute of Drug Discovery and Development, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, No. 22, Qixiangtai Road, Heping District, Tianjin 300070, China
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21
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Guo Y, Xu Y, Dong X, Zhang J. Cross the Undruggable Barrier, the Development of SHP2 Inhibitors: From Catalytic Site Inhibitors to Allosteric Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202100186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yu Guo
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Yaping Xu
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Jianjun Zhang
- Department of Pharmacy Institution The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine) Hangzhou 310006 P.R. China
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22
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Nian Q, Zeng J, He L, Chen Y, Zhang Z, Rodrigues-Lima F, Zhao L, Feng X, Shi J. A small molecule inhibitor targeting SHP2 mutations for the lung carcinoma. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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23
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Mycotoxins as inhibitors of protein tyrosine phosphatases from the deep-sea-derived fungus Aspergillus puniceus SCSIO z021. Bioorg Chem 2020; 107:104571. [PMID: 33373758 DOI: 10.1016/j.bioorg.2020.104571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Nine new xanthone-type and anthraquinone-type mycotoxins including austocystins J-N (1-5), 7-chloro versicolorin A (6), 3'-hydroxy-8-O-methyl versicolorin B (7), 8-O-methyl versiconol (8) and 2',3'-dihydroxy versiconol (9), together with 17 known analogues (10-26) were isolated from an extract of the deep-sea-derived fungus Aspergillus puniceus SCSIO z021. Their structures were elucidated by detailed analysis of spectroscopic data, and their absolute configurations were further determined by quantum chemical calculations of ECD spectra or comparison of the experimental ECD spectra. Eleven hydrogenated austocystins were synthesized from 1-2, 10-15 and 17 by catalytic hydrogenation for bioactivities evaluation. Totally, 18 of the all 37 compounds showed strong toxicity against brine shrimps or Vero cell, and the toxicity of 8-O-methyldemethylsterigmatocystin (18) (LC50 = 0.020 µM) against brine shrimps was higher than those of three positive controls. In addition, 22 of the isolated compounds also exhibited significant inhibitory activity against seven different protein tyrosine phosphatases (PTPs), among them austocystin H (15) and methyl-averantin (24) were the most potent inhibitors with IC50 values of 0.20-3.0 µM. Their structure-bioactivity relationship was also discussed.
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24
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Mostinski Y, Heynen GJJE, López-Alberca MP, Paul J, Miksche S, Radetzki S, Schaller D, Shanina E, Seyffarth C, Kolomeets Y, Ziebart N, de Schryver J, Oestreich S, Neuenschwander M, Roske Y, Heinemann U, Rademacher C, Volkamer A, von Kries JP, Birchmeier W, Nazaré M. From Pyrazolones to Azaindoles: Evolution of Active-Site SHP2 Inhibitors Based on Scaffold Hopping and Bioisosteric Replacement. J Med Chem 2020; 63:14780-14804. [PMID: 33210922 DOI: 10.1021/acs.jmedchem.0c01265] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The tyrosine phosphatase SHP2 controls the activity of pivotal signaling pathways, including MAPK, JAK-STAT, and PI3K-Akt. Aberrant SHP2 activity leads to uncontrolled cell proliferation, tumorigenesis, and metastasis. SHP2 signaling was recently linked to drug resistance against cancer medications such as MEK and BRAF inhibitors. In this work, we present the development of a novel class of azaindole SHP2 inhibitors. We applied scaffold hopping and bioisosteric replacement concepts to eliminate unwanted structural motifs and to improve the inhibitor characteristics of the previously reported pyrazolone SHP2 inhibitors. The most potent azaindole 45 inhibits SHP2 with an IC50 = 0.031 μM in an enzymatic assay and with an IC50 = 2.6 μM in human pancreas cells (HPAF-II). Evaluation in a series of cellular assays for metastasis and drug resistance demonstrated efficient SHP2 blockade. Finally, 45 inhibited proliferation of two cancer cell lines that are resistant to cancer drugs and diminished ERK signaling.
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Affiliation(s)
- Yelena Mostinski
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Guus J J E Heynen
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Maria Pascual López-Alberca
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jerome Paul
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sandra Miksche
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - David Schaller
- Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Elena Shanina
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg, 1, 14476 Potsdam, Germany
| | - Carola Seyffarth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Yuliya Kolomeets
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Nandor Ziebart
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Judith de Schryver
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sylvia Oestreich
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christoph Rademacher
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg, 1, 14476 Potsdam, Germany
| | - Andrea Volkamer
- Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Walter Birchmeier
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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25
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Tripathi RKP, Ayyannan SR. Emerging chemical scaffolds with potential SHP2 phosphatase inhibitory capabilities - A comprehensive review. Chem Biol Drug Des 2020; 97:721-773. [PMID: 33191603 DOI: 10.1111/cbdd.13807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
The drug discovery panorama is cluttered with promising therapeutic targets that have been deserted because of inadequate authentication and screening failures. Molecular targets formerly tagged as "undruggable" are nowadays being more cautiously cross-examined, and whilst they stay intriguing, numerous targets are emerging more accessible. Protein tyrosine phosphatases (PTPs) excellently exemplifies a class of molecular targets that have transpired as druggable, with several small molecules and antibodies recently turned available for further development. In this respect, SHP2, a PTP, has emerged as one of the potential targets in the current pharmacological research, particularly for cancer, due to its critical role in various signalling pathways. Recently, few molecules with excellent potency have entered clinical trials, but none could reach the clinic. Consequently, search for novel, non-toxic, and specific SHP2 inhibitors are on purview. In this review, general aspects of SHP2 including its structure and mechanistic role in carcinogenesis have been presented. It also sheds light on the development of novel molecular architectures belonging to diverse chemical classes that have been proposed as SHP2-specific inhibitors along with their structure-activity relationships (SARs), stemming from chemical, mechanism-based and computer-aided studies reported since January 2015 to July 2020 (excluding patents), focusing on their potency and selectivity. The encyclopedic facts and discussions presented herein will hopefully facilitate researchers to design new ligands with better efficacy and selectivity against SHP2.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Department of Pharmaceutical Science, Sushruta School of Medical and Paramedical Sciences, Assam University (A Central University), Silchar, Assam, India.,Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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26
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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: 34] [Impact Index Per Article: 8.5] [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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27
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Tang K, Jia YN, Yu B, Liu HM. Medicinal chemistry strategies for the development of protein tyrosine phosphatase SHP2 inhibitors and PROTAC degraders. Eur J Med Chem 2020; 204:112657. [PMID: 32738411 DOI: 10.1016/j.ejmech.2020.112657] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022]
Abstract
As a non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene, the Src homology 2 domain-containing protein tyrosine phosphatase (SHP2) is involved in mitogen-activated protein kinase (MAPK) signaling pathway and contributes to immune surveillance via programmed cell death pathway (PD-1/PD-L1). To date, numerous SHP2 inhibitors have been developed, some of them have advanced into clinical trials. Moreover, the first PROTAC degrader SHP2-D26 has been proved to effectively induce degradation of SHP2, which may open a new avenue for targeted SHP2 therapies. In this review, we systematically summarized the development of SHP2 inhibitors with a particular focus on the structure-activity relationships (SAR) studies, crystal structures or binding models, and their modes of action.
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Affiliation(s)
- Kai Tang
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yao-Nan Jia
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
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28
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Patel AD, Pasha TY, Lunagariya P, Shah U, Bhambharoliya T, Tripathi RKP. A Library of Thiazolidin-4-one Derivatives as Protein Tyrosine Phosphatase 1B (PTP1B) Inhibitors: An Attempt To Discover Novel Antidiabetic Agents. ChemMedChem 2020; 15:1229-1242. [PMID: 32390300 DOI: 10.1002/cmdc.202000055] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/28/2020] [Indexed: 01/18/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an important target for the treatment of diabetes. A series of thiazolidin-4-one derivatives 8-22 was designed, synthesized and investigated as PTP1B inhibitors. The new molecules inhibited PTP1B with IC50 values in the micromolar range. 5-(Furan-2-ylmethylene)-2-(4-nitrophenylimino)thiazolidin-4-one (17) exhibited potency with a competitive type of enzyme inhibition. structure-activity relationship studies revealed various structural facets important for the potency of these analogues. The findings revealed a requirement for a nitro group-including hydrophobic heteroaryl ring for PTP1B inhibition. Molecular docking studies afforded good correlation with experimental results. H-bonding and π-π interactions were responsible for optimal binding and effective stabilization of virtual protein-ligand complexes. Furthermore, in-silico pharmacokinetic properties of test compounds predicted their drug-like characteristics for potential oral use as antidiabetic agents.Additionally, a binding site model demonstrating crucial pharmacophoric characteristics influencing potency and binding affinity of inhibitors has been proposed, which can be employed in the design of future potential PTP1B inhibitors.
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Affiliation(s)
- Ashish D Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Anand, 388421, India.,Department of Pharmaceutical Chemistry Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, 391760, India
| | - Thopallada Y Pasha
- Shri Adichunchanagiri College of Pharmacy, Adichunchanagiri University, B G Nagara, Karnataka, 571448, India
| | - Paras Lunagariya
- Smt. R. D. Gardi B. Pharmacy College, Rajkot, Gujarat, 360110, India
| | - Umang Shah
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Anand, 388421, India
| | - Tushar Bhambharoliya
- Wilson College of Textiles, North Carolina State University, North Carolina, 27606, USA
| | - Rati K P Tripathi
- Department of Pharmaceutical Science Sushruta School of Medical and Paramedical Sciences, Assam University (A Central University), Silchar, Assam, 788011, India.,Department of Pharmaceutical Chemistry Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, 391760, India
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29
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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
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30
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Zhao X, Tian K, He RL, Yau SST. Convex hull principle for classification and phylogeny of eukaryotic proteins. Genomics 2019; 111:1777-1784. [DOI: 10.1016/j.ygeno.2018.11.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/25/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
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Deng H, Ke S, Callender R, Balakrishnan G, Spiro TG, May ER, Brooks CL. Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods. J Phys Chem B 2019; 123:7840-7851. [PMID: 31437399 PMCID: PMC6752976 DOI: 10.1021/acs.jpcb.9b06759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yersinia Protein Tyrosine Phosphatase (YopH) is the most efficient enzyme among all known PTPases and relies on its catalytic loop movements for substrate binding and catalysis. Fluorescence, NMR, and UV resonance Raman (UVRR) techniques have been used to study the thermodynamic and dynamic properties of the loop motions. In this study, a computational approach based on the pathway refinement methods nudged elastic band (NEB) and harmonic Fourier beads (HFB) has been developed to provide structural interpretations for the experimentally observed kinetic processes. In this approach, the minimum potential energy pathways for the loop open/closure conformational changes were determined by NEB using a one-dimensional global coordinate. Two dimensional data analyses of the NEB results were performed as an efficient method to qualitatively evaluate the energetics of transitions along several specific physical coordinates. The free energy barriers for these transitions were then determined more precisely using the HFB method. Kinetic parameters were estimated from the energy barriers using transition state theory and compared against experimentally determined kinetic parameters. When the calculated energy barriers are calibrated by a simple "scaling factor", as have been done in our previous vibrational frequency calculations to explain the ligand frequency shift upon its binding to protein, it is possible to make structural interpretations of several observed enzyme dynamic rates. For example, the nanosecond kinetics observed by fluorescence anisotropy may be assigned to the translational motion of the catalytic loop and microsecond kinetics observed in fluorescence T-jump can be assigned to the loop backbone dihedral angle flipping. Furthermore, we can predict that a Trp354 conformational conversion associated with the loop movements would occur on the tens of nanoseconds time scale, to be verified by future UVRR T-jump studies.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Shan Ke
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | | | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, USA 06269
| | - Charles L. Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109
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SarathKumar B, Lakshmi BS. In silico investigations on the binding efficacy and allosteric mechanism of six different natural product compounds towards PTP1B inhibition through docking and molecular dynamics simulations. J Mol Model 2019; 25:272. [PMID: 31451955 DOI: 10.1007/s00894-019-4172-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 08/16/2019] [Indexed: 01/07/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a major negative regulator of both the insulin and leptin receptor phosphorylation which impacts insulin sensitivity and hence is a major therapeutic target for the treatment of type 2 diabetes and obesity. Identification of PTP1B active site inhibitors has proven to be difficult with none of them clearing the phase II clinical trials. Since the conventional methods of targeting the active site of PTP1B have failed to bring out effective PTP1B inhibitors as potential drugs, recent studies are focussing on identification of potential allosteric inhibitors of PTP1B with better specificity and activity. A complete understanding of the molecular features dynamically involved for allosteric site inhibition is still uncertain, and hence, this study is aimed at evaluating the allosteric effectiveness of six natural compounds isolated from medicinal plants which showed in vitro antidiabetic activity along with PTP1B inhibition. The allosteric binding and inhibition of these compounds are studied using computational methods such as molecular docking, homology modelling and molecular dynamics simulations for a timescale of 100 ns. The molecular dynamics simulations of native PTP1B, along with the modelled allosteric α-7 helix, for a timescale of 100 ns, revealed the spontaneous transition of the native PTP1B from open WPD loop (active) to closed WPD loop (inactive) conformations during the simulations. Similar dynamics was observed in the presence of the active site substrate pTyr (phosphotyrosine), whereas this transition was inhibited in the presence of the compounds at the allosteric site. Results of molecular dynamics simulations and principal component analysis reveal that the hindrance to WPD loop was mediated through structural interactions between the allosteric α-helical triad with Loop11 and WPD loop. The MM-PBSA (Molecular Mechanics - Poisson Boltzmann with Surface Area solvation) binding energy results along with H-bonding analysis show the possible allosteric inhibition of Aloe emodin glycoside (AEG), 3β-taraxerol (3BT), chlorogenic acid (CGA) and cichoric acid (CHA) to be higher in comparison with (3β)-stigmast-5-en-3-ol (SGS) and methyl lignocerate (MLG). The interaction analysis was further validated by scoring the allosteric complexes before and after MD simulations using Glide. These findings on spontaneous PTP1B fluctuations and the allosteric interactions provide a better insight into the role of PTP1B fluctuations in impacting the binding energy of allosteric inhibitors towards optimal drug designing for PTP1B. Graphical abstract.
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Affiliation(s)
- Baskaran SarathKumar
- Department of Biotechnology, Anna University, Chennai, Tamil Nadu, 600 025, India
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33
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Wu J, Sun Y, Zhou H, Ma Y, Wang R. Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes. J Biomol Struct Dyn 2019; 38:3156-3165. [PMID: 31402760 DOI: 10.1080/07391102.2019.1654410] [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] [Indexed: 10/26/2022]
Abstract
PTP-MEG2 plays a significant role in insulin production and is able to enhance insulin signaling and improve insulin sensitivity. So, PTP-MEG2 inhibitors are closely associated with type 2 diabetes therapy. A series of novel (R)-5-methylthiazolidin-4-one derivatives were designed and synthesized, and their PTP-MEG2 inhibitory activities (IC50) were determined. Among the desired compounds, 1h shares the highest inhibitory activity (IC50 = 1.34 μM) against PTP-MEG2. Additionally, various post-dynamic analyses confirmed that when compound 1h bound to the PTP-MEG2, the protein conformations became unstable and the function of the pTyr recognition loop (Asn331-Cys338) would be disturbed. And thus, the ideal conformations needed for the catalytic activity was difficult to be maintained. In brief, these might be how the compound 1h worked. Furthermore, we also found that the key residues Arg332 would play a critical role in disturbing the residue interactions. AbbreviationsDCCMdynamic cross-correlation mappingDMFN,N-dimethylformamideDSSPdefinition of secondary structure of proteinsFOXOforkhead transcription factorsMDmolecular dynamicsPCAprincipal component analysisPDBprotein data bankPTKsprotein tyrosine kinasesPTPsprotein tyrosine phosphatasesPTP-MEG2megakaryocyte protein tyrosine phosphatase 2RINresidue interaction networkRINGResidue Interaction Network GeneratorRMSDroot means square deviationRMSFroot mean square fluctuationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Yingzhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hui Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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34
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Peng Y, Sun Q, Park Y. The Bioactive Effects of Chicoric Acid As a Functional Food Ingredient. J Med Food 2019; 22:645-652. [DOI: 10.1089/jmf.2018.0211] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Ye Peng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Quancai Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yeonhwa Park
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
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35
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Alsayed SSR, Beh CC, Foster NR, Payne AD, Yu Y, Gunosewoyo H. Kinase Targets for Mycolic Acid Biosynthesis in Mycobacterium tuberculosis. Curr Mol Pharmacol 2019; 12:27-49. [PMID: 30360731 DOI: 10.2174/1874467211666181025141114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mycolic acids (MAs) are the characteristic, integral building blocks for the mycomembrane belonging to the insidious bacterial pathogen Mycobacterium tuberculosis (M.tb). These C60-C90 long α-alkyl-β-hydroxylated fatty acids provide protection to the tubercle bacilli against the outside threats, thus allowing its survival, virulence and resistance to the current antibacterial agents. In the post-genomic era, progress has been made towards understanding the crucial enzymatic machineries involved in the biosynthesis of MAs in M.tb. However, gaps still remain in the exact role of the phosphorylation and dephosphorylation of regulatory mechanisms within these systems. To date, a total of 11 serine-threonine protein kinases (STPKs) are found in M.tb. Most enzymes implicated in the MAs synthesis were found to be phosphorylated in vitro and/or in vivo. For instance, phosphorylation of KasA, KasB, mtFabH, InhA, MabA, and FadD32 downregulated their enzymatic activity, while phosphorylation of VirS increased its enzymatic activity. These observations suggest that the kinases and phosphatases system could play a role in M.tb adaptive responses and survival mechanisms in the human host. As the mycobacterial STPKs do not share a high sequence homology to the human's, there have been some early drug discovery efforts towards developing potent and selective inhibitors. OBJECTIVE Recent updates to the kinases and phosphatases involved in the regulation of MAs biosynthesis will be presented in this mini-review, including their known small molecule inhibitors. CONCLUSION Mycobacterial kinases and phosphatases involved in the MAs regulation may serve as a useful avenue for antitubercular therapy.
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Affiliation(s)
- Shahinda S R Alsayed
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia
| | - Chau C Beh
- Western Australia School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Bentley 6102 WA, Australia.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, United States
| | - Neil R Foster
- Western Australia School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Bentley 6102 WA, Australia
| | - Alan D Payne
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Yu Yu
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia
| | - Hendra Gunosewoyo
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia
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Discovery of 1,3-diphenyl-1H-pyrazole derivatives containing rhodanine-3-alkanoic acid groups as potential PTP1B inhibitors. Bioorg Med Chem Lett 2019; 29:1187-1193. [DOI: 10.1016/j.bmcl.2019.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/19/2022]
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37
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Docking- and pharmacophore-based virtual screening for the identification of novel Mycobacterium tuberculosis protein tyrosine phosphatase B (MptpB) inhibitor with a thiobarbiturate scaffold. Bioorg Chem 2019; 85:229-239. [DOI: 10.1016/j.bioorg.2018.12.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/23/2018] [Accepted: 12/29/2018] [Indexed: 01/15/2023]
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38
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Xie F, Yang F, Liang Y, Li L, Xia Y, Jiang F, Liu W, Qi Y, Chowdhury SR, Xie D, Fu L. Investigation of stereoisomeric bisarylethenesulfonic acid esters for discovering potent and selective PTP1B inhibitors. Eur J Med Chem 2019; 164:408-422. [DOI: 10.1016/j.ejmech.2018.12.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 01/03/2023]
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Xue W, Tian J, Wang XS, Xia J, Wu S. Discovery of potent PTP1B inhibitors via structure-based drug design, synthesis and in vitro bioassay of Norathyriol derivatives. Bioorg Chem 2019; 86:224-234. [PMID: 30716620 DOI: 10.1016/j.bioorg.2019.01.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/11/2019] [Accepted: 01/27/2019] [Indexed: 12/11/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has recently been identified as a potential target of Norathyriol. Unfortunately, Norathyriol is not a potent PTP1B inhibitor, which somewhat hinders its further application. Based on the fact that no study on the relationship of chemical structure and PTP1B inhibitory activity of Norathyriol has been reported so far, we attempted to perform structural optimization so as to improve the potency for PTP1B. Via structure-based drug design (SBDD), a rational strategy based on the binding mode of Norathyriol to PTP1B, we designed 26 derivatives with substitutions at the four phenolic hydroxyl groups of Norathyriol. By chemical synthesis and in vitro bioassay, we identified seven PTP1B inhibitors that were more potent than Norathyriol, of which XWJ24 showed the highest potency (IC50: 0.6 μM). We also found out that XWJ24 was a competitive inhibitor and showed the 4.5-fold selectivity over its close homolog, TC-PTP. Through molecular docking of XWJ24 against PTP1B, we highlighted the essential role of its hydrogen bond with Asp181 for PTP1B inhibition and identified a potential halogen bond with Asp48 that was not observed for Norathyriol. The current data indicate that our SBDD strategy is effective to discover potent PTP1B-targeted Norathyriol derivatives, and XWJ24 is a promising lead compound for further development.
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Affiliation(s)
- Wenjie Xue
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinlong Tian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiang Simon Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington DC 20059, USA
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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40
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Pan D, Zhang X, Zheng H, Zheng Z, Nong X, Liang X, Ma X, Qi S. Novel anthraquinone derivatives as inhibitors of protein tyrosine phosphatases and indoleamine 2,3-dioxygenase 1 from the deep-sea derived fungusAlternaria tenuissimaDFFSCS013. Org Chem Front 2019. [DOI: 10.1039/c9qo00775j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A novel hydroanthraquinone possessing an unprecedented hexacyclic spiro-fused ring system, anthrininone A (1), and two new anthraquinones, anthrininones B and C (2and3), were obtained from the deep-sea derived fungusAlternaria tenuissima.
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Affiliation(s)
- Dongyan Pan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- Institution of South China Sea Ecology and Environmental Engineering
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
| | - Xuexia Zhang
- New Drug Research & Development Co
- Ltd
- North China Pharmaceutical Group Corporation
- Shijiazhuang
- China
| | - Haizhou Zheng
- New Drug Research & Development Co
- Ltd
- North China Pharmaceutical Group Corporation
- Shijiazhuang
- China
| | - Zhihui Zheng
- New Drug Research & Development Co
- Ltd
- North China Pharmaceutical Group Corporation
- Shijiazhuang
- China
| | - Xuhua Nong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- Institution of South China Sea Ecology and Environmental Engineering
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
| | - Xiao Liang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- Institution of South China Sea Ecology and Environmental Engineering
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
| | - Xuan Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- Institution of South China Sea Ecology and Environmental Engineering
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
| | - Shuhua Qi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- Institution of South China Sea Ecology and Environmental Engineering
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
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41
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Farrokhzadeh A, Akher FB, Soliman MES. Probing the Dynamic Mechanism of Uncommon Allosteric Inhibitors Optimized to Enhance Drug Selectivity of SHP2 with Therapeutic Potential for Cancer Treatment. Appl Biochem Biotechnol 2018; 188:260-281. [DOI: 10.1007/s12010-018-2914-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023]
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42
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Vauzour D, Corsini S, Müller M, Spencer JP. Inhibition of PP2A by hesperetin may contribute to Akt and ERK1/2 activation status in cortical neurons. Arch Biochem Biophys 2018; 650:14-21. [DOI: 10.1016/j.abb.2018.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/27/2018] [Accepted: 04/29/2018] [Indexed: 01/09/2023]
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43
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Baek M, Kim M, Lim JS, Morales LD, Hernandez J, Mummidi S, Williams-Blangero S, Jang IS, Tsin AT, Kim DJ. Epidermal-specific deletion of TC-PTP promotes UVB-induced epidermal cell survival through the regulation of Flk-1/JNK signaling. Cell Death Dis 2018; 9:730. [PMID: 29955047 PMCID: PMC6023867 DOI: 10.1038/s41419-018-0781-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 06/04/2018] [Indexed: 01/27/2023]
Abstract
UVB exposure can contribute to the development of skin cancer by modulating protein tyrosine kinase (PTK) signaling. It has been suggested that UVB radiation increases the ligand-dependent activation of PTKs and induces PTP inactivation. Our recent studies have shown that T-cell protein tyrosine phosphatase (TC-PTP) attenuates skin carcinogenesis induced by chemical regimens, which indicates its critical role in the prevention of skin cancer. In the current work, we report that TC-PTP increases keratinocyte susceptibility to UVB-induced apoptosis via the downregulation of Flk-1/JNK signaling. We showed that loss of TC-PTP led to resistance to UVB-induced apoptosis in vivo epidermis. We established immortalized primary keratinocytes (IPKs) from epidermal-specific TC-PTP-deficient (K14Cre.Ptpn2fl/fl) mice. Immortalized TC-PTP-deficient keratinocytes (TC-PTP/KO IPKs) showed increased cell survival against UVB-induced apoptosis which was concomitant with a UVB-mediated increase in Flk-1 phosphorylation, especially on tyrosine residue 1173. Inhibition of Flk-1 by either its specific inhibitors or siRNA in TC-PTP/KO IPKs reversed this effect and significantly increased cell death after UVB irradiation in comparison with untreated TC-PTP/KO IPKs. Immunoprecipitation analysis using the TC-PTP substrate-trapping mutant TCPTP-D182A indicated that TC-PTP directly interacts with Flk-1 to dephosphorylate it and their interaction was stimulated by UVB. Following UVB-mediated Flk-1 activation, the level of JNK phosphorylation was also significantly increased in TC-PTP/KO IPKs compared to control IPKs. Similar to our results with Flk-1, treatment of TC-PTP/KO IPKs with the JNK inhibitor SP600125 significantly increased apoptosis after UVB irradiation, confirming that the effect of TC-PTP on UVB-mediated apoptosis is regulated by Flk-1/JNK signaling. Western blot analysis showed that both phosphorylated Flk-1 and phosphorylated JNK were significantly increased in the epidermis of TC-PTP-deficient mice compared to control mice following UVB. Our results suggest that TC-PTP plays a protective role against UVB-induced keratinocyte cell damage by promoting apoptosis via negative regulation of Flk-1/JNK survival signaling.
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Affiliation(s)
- Minwoo Baek
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,College of Pharmacy, University of Minnesota, Duluth, MN, USA
| | - Mihwa Kim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Jae Sung Lim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Liza D Morales
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Joselin Hernandez
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Srinivas Mummidi
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Sarah Williams-Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.,South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Ik-Soon Jang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, 305-333, Republic of Korea
| | - Andrew T Tsin
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Dae Joon Kim
- Department of Biomedical Sciences, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA. .,Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA.
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Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife 2018; 7:36307. [PMID: 29877794 PMCID: PMC6039181 DOI: 10.7554/elife.36307] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022] Open
Abstract
Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. Proteins perform many important jobs in each of the cells in our bodies, such as transporting other molecules and helping chemical reactions to occur. The part of the protein directly involved in these tasks is called the active site. Other areas of the protein can communicate with the active site to switch the protein on or off. This method of control is known as allostery. Switching proteins on and off could help us to develop treatments for certain diseases. For example, a protein called PTP1B reduces how well cells can respond to insulin. Switching this protein off could therefore help to treat diabetes. However, much like it’s hard to guess how a light switch is wired to a light bulb without seeing behind the walls, it is hard to predict which remote areas of a protein are ‘wired’ to the active site. Keedy, Hill et al. have now used two complementary methods to examine the structure of PTP1B and find new allosteric sites. The first method captured a series of X-ray images from crystallized molecules of the protein held at different temperatures. This revealed areas of PTP1B that can move like windshield wipers to communicate with each other. The second method soaked PTP1B crystals in trays with hundreds of drug-sized molecules and assessed which sites on the protein the molecules bound to. The molecules generally bound to just a few sites of the protein. Further tests on one of these sites showed that it can communicate with the active site to turn the protein on or off. Further work will be needed to develop drugs that could treat diabetes by binding to the newly identified allosteric sites in PTP1B. More generally, the methods developed by Keedy, Hill et al. could be used to study allostery in other important proteins.
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Zachary B Hill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Emily Kang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - T Justin Rettenmaier
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | | | - Nicholas M Pearce
- Crystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Frank von Delft
- Diamond Light Source, Didcot, United Kingdom.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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45
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Ma Y, Wei HY, Zhang YZ, Jin WY, Li HL, Zhou H, Cheng XC, Wang RL. Synthesis, bioactivity, 3D-QSAR studies of novel dibenzofuran derivatives as PTP-MEG2 inhibitors. Oncotarget 2018; 8:38466-38481. [PMID: 28388567 PMCID: PMC5503546 DOI: 10.18632/oncotarget.16595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/17/2017] [Indexed: 11/25/2022] Open
Abstract
PTP-MEG2 plays a critical role in the diverse cell signalling processes, so targeting PTP-MEG2 is a promising strategy for various human diseases treatments. In this study, a series of novel dibenzofuran derivatives was synthesized and assayed for their PTP-MEG2 inhibitory activities. 10a with highest inhibitory activity (320 nM) exhibited significant selectivity for PTP-MEG2 over its close homolog SHP2, CDC25 (IC50 > 50 μM). By means of the powerful “HipHop” technique, a 3D-QSAR study was carried out to explore structure activity relationship of these molecules. The generated pharmacophore model revealed that the one RA, three Hyd, and two HBA features play an important role in binding to the active site of the target protein-PTP-MEG2. Docking simulation study indicated that 10a achieved its potency and specificity for PTP-MEG2 by targeting unique nearby peripheral binding pockets and the active site. The absorption, distribution, metabolism and excretion (ADME) predictions showed that the 11 compounds hold high potential to be novel lead compounds for targeting PTP-MEG2. Our findings here can provide a new strategy or useful insights for designing the effective PTP-MEG2 inhibitors.
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Affiliation(s)
- Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hui-Yu Wei
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China.,Eye Hospital, Tianjin Medical University, School of Optometry and Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Yu-Ze Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Yan Jin
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hui Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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46
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Li ZP, Lee HH, Uddin Z, Song YH, Park KH. Caged xanthones displaying protein tyrosine phosphatase 1B (PTP1B) inhibition from Cratoxylum cochinchinense. Bioorg Chem 2018. [PMID: 29533213 DOI: 10.1016/j.bioorg.2018.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Four new caged xanthones (1-4) and two known compounds (5, 6) were isolated from the roots of Cratoxylum cochinchinense, a polyphenol rich plant, collected in China. The structures of the isolated compounds (1-6) were characterized by obtaining their detailed spectroscopic data. In particular, compounds 1 and 6 were fully identified by X-ray crystallographic data. The isolated compounds (1-6) were evaluated against protein tyrosine phosphatase 1B (PTP1B), which plays an important role in diabetes, obesity, and cancer. Among these compounds, 3, 4, and 6 displayed significant inhibition with IC50 values of 76.3, 43.2, and 6.6 µM, respectively. A detailed kinetic study was conducted by determining Km, Vmax, and the ratio of Kik and Kiv, which revealed that all the compounds behaved as competitive inhibitors.
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Affiliation(s)
- Zuo Peng Li
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hyeong-Hwan Lee
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Zia Uddin
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yeong Hun Song
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ki Hun Park
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea.
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47
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Inhibition of protein tyrosine phosphatase 1B (PTP1B) and α-glucosidase by xanthones from Cratoxylum cochinchinense, and their kinetic characterization. Bioorg Med Chem 2018; 26:737-746. [DOI: 10.1016/j.bmc.2017.12.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/17/2017] [Accepted: 12/24/2017] [Indexed: 11/18/2022]
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48
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Wang M, Li X, Dong L, Chen X, Xu W, Wang R. Virtual screening, optimization, and identification of a novel specific PTP-MEG2 Inhibitor with potential therapy for T2DM. Oncotarget 2018; 7:50828-50834. [PMID: 27384997 PMCID: PMC5239439 DOI: 10.18632/oncotarget.10341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/03/2016] [Indexed: 11/25/2022] Open
Abstract
Megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) is a tyrosine phosphatase expressed in megakaryocytic cells, and causes insulin sensitization when down regulated. Therefore, specific inhibitors of PTP-MEG2 are potential candidates for novel Type 2 Diabetes (T2DM)therapy. In this study, we discovered PTP-MEG2 inhibitors using high throughput and virtual screening (HTS/VS) and structural optimization in silicon. Eight compound-candidates were identified from the interactions with PTP-MEG2, protein tyrosine phosphatase 1B (PTP1B) and T cell protein tyrosine phosphatase (TCPTP). Results from enzymatic assays show compounds 4a and 4b inhibited PTP-MEG2 activity with an IC50 of 3.2 μM and 4.3 μM, respectively. Further, they showed a 7.5 and 5.5 fold change against PTP1B and TCPTP, respectively. We propose compounds 4a and 4b are PTP-MEG2 inhibitors with potential therapeutic use in T2DM treatment.
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Affiliation(s)
- Meiyan Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiaobo Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lei Dong
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Xiubo Chen
- Tianjin Medical University Eye Hospital, Tianjin, China
| | - Weiren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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49
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Dadmal TL, Appalanaidu K, Kumbhare RM, Mondal T, Ramaiah MJ, Bhadra MP. Synthesis and biological evaluation of triazole and isoxazole-tagged benzothiazole/benzoxazole derivatives as potent cytotoxic agents. NEW J CHEM 2018. [DOI: 10.1039/c8nj01249k] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cancer is a major health problem and the most upsetting disease in humans, leading to death in both developed and developing countries.
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Affiliation(s)
- Tulshiram L. Dadmal
- Fluoroorganic Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Government of Maharashtra's
| | - K. Appalanaidu
- Fluoroorganic Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
| | - Ravindra M. Kumbhare
- Fluoroorganic Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
| | - Tanmoy Mondal
- Centre for Chemical Biology
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| | - M. Janaki Ramaiah
- Centre for Chemical Biology
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
- School of Chemical and Biotechnology
| | - Manika Pal Bhadra
- Centre for Chemical Biology
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
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50
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Xie J, Si X, Gu S, Wang M, Shen J, Li H, Shen J, Li D, Fang Y, Liu C, Zhu J. Allosteric Inhibitors of SHP2 with Therapeutic Potential for Cancer Treatment. J Med Chem 2017; 60:10205-10219. [DOI: 10.1021/acs.jmedchem.7b01520] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jingjing Xie
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan
District, Beijing 100049, China
| | - Xiaojia Si
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer
Feld 270, 69120 Heidelberg, Germany
| | - Shoulai Gu
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
| | - Mingliang Wang
- Department of Natural Products Chemistry, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jian Shen
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan
District, Beijing 100049, China
| | - Haoyan Li
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan
District, Beijing 100049, China
| | - Jian Shen
- Viva Biotech Ltd. 334 Aidisheng Road, Shanghai 201203, China
| | - Dan Li
- Key Laboratory for
the Genetics of Developmental and Neuropsychiatric Disorders (Ministry
of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanjia Fang
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
| | - Cong Liu
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
| | - Jidong Zhu
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
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