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Devi B, Vasishta SS, Das B, Baidya ATK, Rampa RS, Mahapatra MK, Kumar R. Integrated use of ligand and structure-based virtual screening, molecular dynamics, free energy calculation and ADME prediction for the identification of potential PTP1B inhibitors. Mol Divers 2024; 28:649-669. [PMID: 36745307 DOI: 10.1007/s11030-023-10608-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are the group of enzymes that control both cellular activity and the dephosphorylation of tyrosine (Tyr)-phosphorylated proteins. Dysregulation of PTP1B has contributed to numerous diseases including Diabetes Mellitus, Alzheimer's disease, and obesity rendering PTP1B as a legitimate target for therapeutic applications. It is highly challenging to target this enzyme because of its highly conserved and positively charged active-site pocket motivating researchers to find novel lead compounds against it. The present work makes use of an integrated approach combining ligand-based and structure-based virtual screening to find hit compounds targeting PTP1B. Initially, pharmacophore modeling was performed to find common features like two hydrogen bond acceptors, an aromatic ring and one hydrogen bond donor from the potent PTP1B inhibitors. The dataset of compounds matching with the common pharmacophoric features was filtered to remove Pan-Assay Interference substructure and to match the Lipinski criteria. Then, compounds were further prioritized using molecular docking and top fifty compounds with good binding affinity were selected for absorption, distribution, metabolism, and excretion (ADME) predictions. The top five compounds with high solubility, absorption and permeability holding score of - 10 to - 9.3 kcal/mol along with Ertiprotafib were submitted to all-atom molecular dynamic (MD) studies. The MD studies and binding free energy calculations showed that compound M4, M5 and M8 were having better binding affinity for PTP1B enzyme with ∆Gtotal score of - 24.25, - 31.47 and - 33.81 kcal/mol respectively than other compounds indicating that compound M8 could be a suitable lead compound as PTP1B inhibitor.
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Affiliation(s)
- Bharti Devi
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Sumukh Satyanarayana Vasishta
- Department of Chemical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Bhanuranjan Das
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Anurag T K Baidya
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | - Rahul Salmon Rampa
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India
| | | | - Rajnish Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP, 221005, India.
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Computational Methods in Cooperation with Experimental Approaches to Design Protein Tyrosine Phosphatase 1B Inhibitors in Type 2 Diabetes Drug Design: A Review of the Achievements of This Century. Pharmaceuticals (Basel) 2022; 15:ph15070866. [PMID: 35890163 PMCID: PMC9322956 DOI: 10.3390/ph15070866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) dephosphorylates phosphotyrosine residues and is an important regulator of several signaling pathways, such as insulin, leptin, and the ErbB signaling network, among others. Therefore, this enzyme is considered an attractive target to design new drugs against type 2 diabetes, obesity, and cancer. To date, a wide variety of PTP1B inhibitors that have been developed by experimental and computational approaches. In this review, we summarize the achievements with respect to PTP1B inhibitors discovered by applying computer-assisted drug design methodologies (virtual screening, molecular docking, pharmacophore modeling, and quantitative structure–activity relationships (QSAR)) as the principal strategy, in cooperation with experimental approaches, covering articles published from the beginning of the century until the time this review was submitted, with a focus on studies conducted with the aim of discovering new drugs against type 2 diabetes. This review encourages the use of computational techniques and includes helpful information that increases the knowledge generated to date about PTP1B inhibition, with a positive impact on the route toward obtaining a new drug against type 2 diabetes with PTP1B as a molecular target.
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Liu R, Mathieu C, Berthelet J, Zhang W, Dupret JM, Rodrigues Lima F. Human Protein Tyrosine Phosphatase 1B (PTP1B): From Structure to Clinical Inhibitor Perspectives. Int J Mol Sci 2022; 23:ijms23137027. [PMID: 35806030 PMCID: PMC9266911 DOI: 10.3390/ijms23137027] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation is an essential process in biological events and is considered critical for biological functions. In tissues, protein phosphorylation mainly occurs on tyrosine (Tyr), serine (Ser) and threonine (Thr) residues. The balance between phosphorylation and dephosphorylation is under the control of two super enzyme families, protein kinases (PKs) and protein phosphatases (PPs), respectively. Although there are many selective and effective drugs targeting phosphokinases, developing drugs targeting phosphatases is challenging. PTP1B, one of the most central protein tyrosine phosphatases (PTPs), is a key player in several human diseases and disorders, such as diabetes, obesity, and hematopoietic malignancies, through modulation of different signaling pathways. However, due to high conservation among PTPs, most PTP1B inhibitors lack specificity, raising the need to develop new strategies targeting this enzyme. In this mini-review, we summarize three classes of PTP1B inhibitors with different mechanisms: (1) targeting multiple aryl-phosphorylation sites including the catalytic site of PTP1B; (2) targeting allosteric sites of PTP1B; (3) targeting specific mRNA sequence of PTP1B. All three types of PTP1B inhibitors present good specificity over other PTPs and are promising for the development of efficient small molecules targeting this enzyme.
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Affiliation(s)
- Rongxing Liu
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
| | | | - Jérémy Berthelet
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
- Centre Epigénétique et Destin Cellulaire, Université Paris Cité, CNRS, F-75013 Paris, France
| | - Wenchao Zhang
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jean-Marie Dupret
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
| | - Fernando Rodrigues Lima
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université Paris Cité, F-75013 Paris, France; (R.L.); (J.B.); (W.Z.); (J.-M.D.)
- Correspondence:
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Inhibition Mechanism of Components Isolated from Morus alba Branches on Diabetes and Diabetic Complications via Experimental and Molecular Docking Analyses. Antioxidants (Basel) 2022; 11:antiox11020383. [PMID: 35204264 PMCID: PMC8869400 DOI: 10.3390/antiox11020383] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Previously, we reported the anti-diabetic effect of Morus alba root bark and the compounds therein. In our continuous study of other parts of this plant, the ability of the branch of Morus alba to inhibit α-glucosidase, protein tyrosine phosphatase 1B (PTP1B), and advanced glycation end products (AGEs) formation was evaluated. Moreover, there are no previous studies that have performed enzyme kinetics and molecular docking analyses, along with assessments of peroxynitrite (ONOO−) inhibitory activities. Since the Morus alba branch exhibited favorable inhibitory effects, repeated column chromatography was performed to obtain eight compounds, including four flavonoids (1, 3, 6, 8), one arylbenzofuran (2), one stilbene (5), one Diels–Alder-type adduct (7), and one sterol (4). Among them, compounds 1–3 and 5–7 were mixed-type inhibitors of α-glucosidase, sharing the same catalytic residues with acarbose and the same allosteric sites with (Z)-3-bytylidenephthalide. On the other hand, kuwanon C (1) and oxyresveratrol (5) interacted with residues of the allosteric site (α3 and α6 helices) of PTP1B, indicating their use as non-competitive inhibitors. Interestingly, kuwanon G (7) directly bound the catalytic site, or interrupted the binding between the substrate and the active site, as a mixed-type inhibitor. Moreover, most of the compounds exhibited greater activity against AGE formation and ONOO− than positive controls. The IC50 values required to inhibit ONOO− using compounds 1, 3, 5, 6, and 7 were reported for the first time, and range from 1.08 to 12.92 μM. Based on the structure–activity relationship, the presence of hydroxyl, resorcinol, and prenyl moieties was important in the prevention of diabetes’ pathological mechanisms, and these findings have been further supported by molecular docking analysis. These computational and experimental results will be useful in the development of therapeutic candidates to prevent/treat diabetes and its complications.
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Recent Updates on Development of Protein-Tyrosine Phosphatase 1B Inhibitors for Treatment of Diabetes, Obesity and Related Disorders. Bioorg Chem 2022; 121:105626. [DOI: 10.1016/j.bioorg.2022.105626] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/19/2021] [Accepted: 01/13/2022] [Indexed: 01/30/2023]
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Elhassan RM, Hou X, Fang H. Recent advances in the development of allosteric protein tyrosine phosphatase inhibitors for drug discovery. Med Res Rev 2021; 42:1064-1110. [PMID: 34791703 DOI: 10.1002/med.21871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 09/26/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023]
Abstract
Protein tyrosine phosphatases (PTPs) superfamily catalyzes tyrosine de-phosphorylation which affects a myriad of cellular processes. Imbalance in signal pathways mediated by PTPs has been associated with development of many human diseases including cancer, metabolic, and immunological diseases. Several compelling evidence suggest that many members of PTP family are novel therapeutic targets. However, the clinical development of conventional PTP-based active-site inhibitors originally was hampered by the poor selectivity and pharmacokinetic properties. In this regard, PTPs has been widely dismissed as "undruggable." Nonetheless, allosteric modulation has become increasingly an influential and alternative approach that can be exploited for drug development against PTPs. Unlike active-site inhibitors, allosteric inhibitors exhibit a remarkable target-selectivity, drug-likeness, potency, and in vivo activity. Intriguingly, there has been a high interest in novel allosteric PTPs inhibitors within the last years. In this review, we focus on the recent advances of allosteric inhibitors that have been explored in drug discovery and have shown an excellent result in the development of PTPs-based therapeutics. A special emphasis is placed on the structure-activity relationship and molecular mechanistic studies illustrating applications in chemical biology and medicinal chemistry.
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Affiliation(s)
- Reham M Elhassan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong, China
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García‐Marín J, Griera M, Alajarín R, Rodríguez‐Puyol M, Rodríguez‐Puyol D, Vaquero JJ. A Computer-Driven Scaffold-Hopping Approach Generating New PTP1B Inhibitors from the Pyrrolo[1,2-a]quinoxaline Core. ChemMedChem 2021; 16:2895-2906. [PMID: 34137509 PMCID: PMC8518816 DOI: 10.1002/cmdc.202100338] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/13/2021] [Indexed: 11/06/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a very promising target for the treatment of metabolic disorders such as type II diabetes mellitus. Although it was validated as a promising target for this disease more than 30 years ago, as yet there is no drug in advanced clinical trials, and its biochemical mechanism and functions are still being studied. In the present study, based on our experience generating PTP1B inhibitors, we have developed and implemented a scaffold-hopping approach to vary the pyrrole ring of the pyrrolo[1,2-a]quinoxaline core, supported by extensive computational techniques aimed to explain the molecular interaction with PTP1B. Using a combination of docking, molecular dynamics and end-point free-energy calculations, we have rationally designed a hypothesis for new PTP1B inhibitors, supporting their recognition mechanism at a molecular level. After the design phase, we were able to easily synthesize proposed candidates and their evaluation against PTP1B was found to be in good concordance with our predictions. Moreover, the best candidates exhibited glucose uptake increments in cellulo model, thus confirming their utility for PTP1B inhibition and validating this approach for inhibitors design and molecules thus obtained.
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Affiliation(s)
- Javier García‐Marín
- Departamento de Química Orgánica y Química InorgánicaUniversidad de Alcalá28805Alcalá de HenaresSpain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Instituto de Investigación Química Andrés Manuel del Río (IQAR)Universidad de AlcaláAlcalá de HenaresSpain
- Departamento de Química Biológica y EstructuralCentro de Investigaciones Biológicas Margarita Salas (CIB-CSIC)Calle Ramiro de Maeztu 928040MadridSpain
| | - Mercedes Griera
- Graphenano Medical Care, S.L.C/Pablo Casals, no. 13YeclaMurciaSpain
- Departamento de Biología de SistemasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Ramón Alajarín
- Departamento de Química Orgánica y Química InorgánicaUniversidad de Alcalá28805Alcalá de HenaresSpain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Instituto de Investigación Química Andrés Manuel del Río (IQAR)Universidad de AlcaláAlcalá de HenaresSpain
| | - Manuel Rodríguez‐Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Departamento de Biología de SistemasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Diego Rodríguez‐Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Fundación de Investigación BiomédicaUnidad de Nefrología del Hospital Príncipe de Asturias yDepartamento de Medicina y Especialidades MédicasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Juan J. Vaquero
- Departamento de Química Orgánica y Química InorgánicaUniversidad de Alcalá28805Alcalá de HenaresSpain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Instituto de Investigación Química Andrés Manuel del Río (IQAR)Universidad de AlcaláAlcalá de HenaresSpain
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Natural α-Glucosidase and Protein Tyrosine Phosphatase 1B Inhibitors: A Source of Scaffold Molecules for Synthesis of New Multitarget Antidiabetic Drugs. Molecules 2021; 26:molecules26164818. [PMID: 34443409 PMCID: PMC8400511 DOI: 10.3390/molecules26164818] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 12/13/2022] Open
Abstract
Diabetes mellitus (DM) represents a group of metabolic disorders that leads to acute and long-term serious complications and is considered a worldwide sanitary emergence. Type 2 diabetes (T2D) represents about 90% of all cases of diabetes, and even if several drugs are actually available for its treatment, in the long term, they show limited effectiveness. Most traditional drugs are designed to act on a specific biological target, but the complexity of the current pathologies has demonstrated that molecules hitting more than one target may be safer and more effective. The purpose of this review is to shed light on the natural compounds known as α-glucosidase and Protein Tyrosine Phosphatase 1B (PTP1B) dual-inhibitors that could be used as lead compounds to generate new multitarget antidiabetic drugs for treatment of T2D.
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Begum N, Nasir A, Parveen Z, Muhammad T, Ahmed A, Farman S, Jamila N, Shah M, Bibi NS, Khurshid A, Huma Z, Khalil AAK, Albrakati A, Batiha GES. Evaluation of the Hypoglycemic Activity of Morchella conica by Targeting Protein Tyrosine Phosphatase 1B. Front Pharmacol 2021; 12:661803. [PMID: 34093192 PMCID: PMC8173442 DOI: 10.3389/fphar.2021.661803] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Morchella conica (M. conica) Pers. is one of six wild edible mushrooms that are widely used by Asian and European countries for their nutritional value. The present study assessed the anti-diabetic potential of M. conica methanolic extract (100 mg/kg body weight) on streptozotocin (STZ)-induced diabetic mice. STZ was used in a single dose of 65 mg/kg to establish diabetic models. Body weights, water/food intake and fasting blood glucose levels were measured. Histopathological analysis of the pancreas and liver were performed to evaluate STZ-induced tissue injuries. In addition, in vitro assays such as α-amylase and protein tyrosine phosphatase 1B (PTP1B) inhibitory, antiglycation, antioxidant and cytotoxicity were performed. The in vitro study indicated potent PTP1B inhibitory potential of M. conica with an IC50 value of 26.5 μg/ml as compared to the positive control, oleanolic acid (IC50 36.2 μg/ml). In vivo investigation showed a gradual decrease in blood sugar level in M. conica-treated mice (132 mg/dl) at a concentration of 100 mg/kg as compared to diabetic mice (346 mg/dl). The extract positively improved liver and kidney damages as were shown by their serum glutamic pyruvic transaminase, serum glutamic oxaloacetate, alkaline phosphatase, serum creatinine and urea levels. Histopathological analysis revealed slight liver and pancreas improvement of mice treated with extract. Cytotoxicity assays displayed lower IC50 values. Based on the present results of the study, it may be inferred that M. conica are rich in bioactive compounds responsible for antidiabetic activity and this mushroom may be a potential source of antidiabetic drug. However, further studies are required in terms of isolation of bioactive compounds to validate the observed results.
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Affiliation(s)
- Naeema Begum
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Nasir
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan.,Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Zahida Parveen
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Taj Muhammad
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Asma Ahmed
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahor, Lahor, Pakistan
| | - Saira Farman
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Nargis Jamila
- Department of Chemistry, Shaheed Benazir Women University of Science and Technology Peshawar, Peshawar, Pakistan
| | - Mohib Shah
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Noor Shad Bibi
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Akif Khurshid
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Zille Huma
- Department of Botany, University of Peshawar, Peshawar, Pakistan
| | - Atif Ali Khan Khalil
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, Taif, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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Yousof Ali M, Jannat S, Mizanur Rahman M. Investigation of C-glycosylated apigenin and luteolin derivatives’ effects on protein tyrosine phosphatase 1B inhibition with molecular and cellular approaches. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.comtox.2020.100141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Ha MT, Shrestha S, Tran TH, Kim JA, Woo MH, Choi JS, Min BS. Inhibition of PTP1B by farnesylated 2-arylbenzofurans isolated from Morus alba root bark: unraveling the mechanism of inhibition based on in vitro and in silico studies. Arch Pharm Res 2020; 43:961-975. [PMID: 32978714 PMCID: PMC7518952 DOI: 10.1007/s12272-020-01269-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/22/2020] [Indexed: 12/24/2022]
Abstract
Among the 2-arylbenzofuran derivatives isolated from Morus alba, the farnesylated 2-arylbenzofuran is a rarer constituent. The derivative has been reported to exert anti-obesity effect; however, its inhibitory effect on protein tyrosine phosphatase 1B (PTP1B) has not been investigated. In the previous study, the presence of the farnesyl group in the structure of 2-arylbenzofurans was found to have positive influences on their pancreatic lipase inhibitory activity. In the present study, we have confirmed the authenticity of the notation based on the PTP1B inhibitory activity of farnesylated 2-arylbenzofurans. Specifically, two farnesylated 2-arylbenzofurans [morusalfurans B (2) and C (3)] showed strong inhibitory effects on PTP1B with IC50 values of 8.92 and 7.26 µM, respectively, which was significantly higher than that of the positive controls [sodium orthovanadate (IC50 = 15.10 µM) and ursolic acid (IC50 = 11.34 µM)]. Besides, two 2-arylbenzofurans [morusalfurans A (1) and F (6)], one flavonoid [morusalnol B (9)], and one geranylated stilbene [morusibene A (11)] exhibited PTP1B inhibition with IC50 values ranging from 11.02 to 26.56 µM. Kinetic studies revealed compounds 2, 3, 6, and 11 as mixed type PTP1B inhibitors, while 1 and 9 are known as noncompetitive. Molecular docking simulations demonstrated that these active compounds can bind with the respective catalytic or/and allosteric sites of PTP1B with negative binding energies and the results are in accordance with that of the kinetic studies. To the best of our knowledge, this is the first time, the PTP1B inhibitory activity of eleven compounds (1–11), as well as the mechanism of action underlying the effects on PTP1B enzyme of the active compounds, were investigated. In vitro and in silico results suggest that the farnesylated 2-arylbenzofurans from M. alba may potentially be utilized as an effective treatment therapy for type 2 diabetes mellitus and its associated complications.
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Affiliation(s)
- Manh Tuan Ha
- College of Pharmacy, Drug Research and Development Center, Daegu Catholic University, 38430, Gyeongbuk, Republic of Korea.,School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Srijan Shrestha
- Department of Food and Life Science, Pukyong National University, 48513, Busan, Republic of Korea.,Discipline of Pharmacology, School of Medicine, Faculty of Health Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thu Huong Tran
- School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Jeong Ah Kim
- College of Pharmacy, Kyungpook National University, 702-701, Daegu, Republic of Korea
| | - Mi Hee Woo
- College of Pharmacy, Drug Research and Development Center, Daegu Catholic University, 38430, Gyeongbuk, Republic of Korea
| | - Jae Sue Choi
- Department of Food and Life Science, Pukyong National University, 48513, Busan, Republic of Korea.
| | - Byung Sun Min
- College of Pharmacy, Drug Research and Development Center, Daegu Catholic University, 38430, Gyeongbuk, Republic of Korea.
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Javier GM. Computational insight into the selective allosteric inhibition for PTP1B versus TCPTP: a molecular modelling study. J Biomol Struct Dyn 2020; 39:5399-5410. [PMID: 32643532 DOI: 10.1080/07391102.2020.1790421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
All over the world, diabetes mellitus type 2 has spread as a problematic pandemic. Despite currently available treatments, approved drugs still show undesirable side effects and loss of efficacy or target symptoms instead of causes. Protein tyrosine phosphatase 1B (PTP1B), since its discovery, has emerged as a very promising target against this disease. Although the information regarding the enzyme is immense, little is known about the selectivity between this enzyme and its closest homologue, lymphocyte T tyrosine phosphatase (TCPTP), which is responsible for complicated side effects. In this study, on the basis of different computational approaches, we are able to highlight the importance of a phenylalanine residue located in PTP1B, but not in TCPTP, as a crucial hotspot that causes selectivity and stability for the whole ligand bound system. These results not only allow to explain the selectivity determinants of PTP1B but also provide a useful guide for the design of new allosteric inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Garcia-Marin Javier
- Facultad de Farmacia, Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Facultad de Farmacia, Instituto de Investigación Química Andrés M. del Río, Universidad de Alcalá, Alcalá de Henares, Spain
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13
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Mphahlele MJ, Choong YS, Maluleka MM, Gildenhuys S. Synthesis, In Vitro Evaluation and Molecular Docking of the 5-Acetyl-2-aryl-6-hydroxybenzo[ b]furans against Multiple Targets Linked to Type 2 Diabetes. Biomolecules 2020; 10:E418. [PMID: 32156083 PMCID: PMC7175131 DOI: 10.3390/biom10030418] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/12/2020] [Accepted: 02/19/2020] [Indexed: 02/06/2023] Open
Abstract
The 5-acetyl-2-aryl-6-hydroxybenzo[b]furans 2a-h have been evaluated through in vitro enzymatic assay against targets which are linked to type 2 diabetes (T2D), namely, α-glucosidase, protein tyrosine phosphatase 1B (PTP1B) and β-secretase. These compounds have also been evaluated for antioxidant activity using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free-radical scavenging method. The most active compounds against α-glucosidase and/or PTP1B, namely, 4-fluorophenyl 2c, 4-methoxyphenyl 2g and 3,5-dimethoxyphenyl substituted 2h derivatives were also evaluated for potential anti-inflammatory properties against cyclooxygenase-2 activity. The Lineweaver-Burk and Dixon plots were used to determine the type of inhibition on compounds 2c and 2h against α-glucosidase and PTP1B receptors. The interactions were investigated in modelled complexes against α-glucosidase and PTP1B via molecular docking.
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Affiliation(s)
- Malose J. Mphahlele
- Department of Chemistry, University of South Africa, Private Bag X06, Florida 1710, South Africa
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia;
| | - Marole M. Maluleka
- Department of Chemistry, University of South Africa, Private Bag X06, Florida 1710, South Africa
| | - Samantha Gildenhuys
- Department of Life & Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X06, Florida 1710, South Africa;
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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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Khan S, Bjij I, Soliman MES. Selective Covalent Inhibition of “Allosteric Cys121” Distort the Binding of PTP1B Enzyme: A Novel Therapeutic Approach for Cancer Treatment. Cell Biochem Biophys 2019; 77:203-211. [DOI: 10.1007/s12013-019-00882-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/09/2019] [Indexed: 02/05/2023]
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Insight into the PTP1B Inhibitory Activity of Arylbenzofurans: An In Vitro and In Silico Study. Molecules 2019; 24:molecules24162893. [PMID: 31395821 PMCID: PMC6721227 DOI: 10.3390/molecules24162893] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) plays a specific role as a negative regulator of insulin signaling pathways and is a validated therapeutic target for Type 2 diabetes. Previously, arylbenzofurans were reported to have inhibitory activity against PTP1B. However, detailed investigation regarding their structure activity relationship (SAR) has not been elucidated. The main aim of this work was to investigate the PTP1B inhibitory activity of 2-arylbenzofuran analogs (sanggenofuran A (SA), mulberrofuran D2 (MD2), mulberrofuran D (MD), morusalfuran B (MB), mulberrofuran H (MH)) isolated from the root bark of Morus alba. All compounds demonstrated potent inhibitory activity with IC50 values ranging from 3.11 to 53.47 µM. Among the tested compounds, MD2 showed the strongest activity (IC50, 3.11 µM), followed by MD and MB, while SA and MH demonstrated the lowest activity. Lineweaver-Burk and Dixon plots were used for the determination of inhibition type whereas ligand and receptor interactions were investigated in modeled complexes via molecular docking. Our study clearly supports 2-arylbenzofuran analogs as a promising class of PTP1B inhibitors and illustrates the key positions responsible for the inhibitory activity, their correlation, the effect of prenyl/geranyl groups, and the influence of resorcinol scaffold, which can be further explored in-depth to develop therapeutic agents against T2DM.
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