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Yang Z, Ying Y, Cheng S, Wu J, Zhang Z, Hu P, Xiong J, Li H, Zeng Q, Cai Z, Feng Y, Fang Y. Discovery of Selective Proteolysis-Targeting Chimera Degraders Targeting PTP1B as Long-Term Hypoglycemic Agents. J Med Chem 2024; 67:7569-7584. [PMID: 38690687 DOI: 10.1021/acs.jmedchem.4c00356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
PTP1B, a promising target for insulin sensitizers in type 2 diabetes treatment, can be effectively degraded using proteolysis-targeting chimera (PROTAC). This approach offers potential for long-acting antidiabetic agents. We report potent bifunctional PROTACs targeting PTP1B through the E3 ubiquitin ligase cereblon. Western blot analysis showed significant PTP1B degradation by PROTACs at concentrations from 5 nM to 5 μM after 48 h. Evaluation of five highly potent PROTACs revealed compound 75 with a longer PEG linker (23 atoms), displaying remarkable degradation activity after 48 and 72 h, with DC50 values of 250 nM and 50 nM, respectively. Compound 75 induced selective degradation of PTP1B, requiring engagement with both the target protein and CRBN E3 ligase, in a ubiquitination and proteasome-dependent manner. It significantly reduced blood glucose AUC0-2h to 29% in an oral glucose tolerance test and activated the IRS-1/PI3K/Akt signaling pathway in HepG2 cells, showing promise for long-term antidiabetic therapy.
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Affiliation(s)
- Zunhua Yang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Yuqi Ying
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Shaobing Cheng
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Jiamin Wu
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Ziwei Zhang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Pei Hu
- Jiangzhong Pharmaceutical Co., Ltd., Nanchang 330103, China
| | - Jian Xiong
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Huilan Li
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Qing Zeng
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Zhifang Cai
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Yulin Feng
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Yuanying Fang
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine, Nanchang 330006, China
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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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Design, synthesis, kinetic, molecular dynamics, and hypoglycemic effect characterization of new and potential selective benzimidazole derivatives as Protein Tyrosine Phosphatase 1B inhibitors. Bioorg Med Chem 2021; 48:116418. [PMID: 34563877 DOI: 10.1016/j.bmc.2021.116418] [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] [Received: 07/08/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022]
Abstract
Protein-tyrosine phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathway and has been validated as a therapeutic target for type 2 diabetes. A wide variety of scaffolds have been included in the structure of PTP1B inhibitors, one of them is the benzimidazole nucleus. Here, we report the design and synthesis of a new series of di- and tri- substituted benzimidazole derivatives including their kinetic and structural characterization as PTP1B inhibitors and hypoglycemic activity. Results show that compounds 43, 44, 45, and 46 are complete mixed type inhibitors with a Ki of 12.6 μM for the most potent (46). SAR type analysis indicates that a chloro substituent at position 6(5), a β-naphthyloxy at position 5(6), and a p-benzoic acid attached to the linker 2-thioacetamido at position 2 of the benzimidazole nucleus, was the best combination for PTP1B inhibition and hypoglycemic activity. In addition, molecular dynamics studies suggest that these compounds could be potential selective inhibitors from other PTPs such as its closest homologous TCPTP, SHP-1, SHP-2 and CDC25B. Therefore, the compounds reported here are good hits that provide structural, kinetic, and biological information that can be used to develop novel and selective PTP1B inhibitors based on benzimidazole scaffold.
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Maheshwari N, Karthikeyan C, Bhadada SV, Verma AK, Sahi C, Moorthy NHN, Trivedi P. Virtual Screening Based Discovery of PTP1B Inhibitors and Their Biological Evaluations. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200826174051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background :
The discovery of novel antidiabetics for the treatment of type 2 diabetes
mellitus (T2DM) is an important task nowadays because the current treatment approaches have certain
limitations. The reported studies showed that the protein tyrosine phosphatase 1B (PTP1B) is a
valuable target, can be used to develop significant antidiabetic molecules.
Objective:
In the present investigation, computational methods and biological evaluation studies have
been applied to develop novel PTP1B inhibitors with good enzyme binding affinity and activity.
Methods:
Virtual screening (docking) analysis of SPECS database compounds on PTP1B enzyme
was performed using Schrodinger software. In vitro and in vivo biological evaluations had been
conducted with the identified hits.
Results:
The results revealed that the molecules identified through these studies have shown significant
interactions with the active site residues of the PTP1B enzyme. The compounds S1 and S2 provided
significant binding interactions with the residues (Arg221 and Gln262) and have shown considerable
in vitro PTP1B inhibitory activity and in vivo antidiabetic activity. The compounds S1 and
S2 possessed 35.44±0.12% and 33.68±0.08% inhibitory activities, respectively.
Conclusion:
These identified hits will be used as a template for design and development of novel
PTP1B inhibitors with a compatible pharmacokinetic profile.
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Affiliation(s)
- Neelesh Maheshwari
- School of Pharmaceutical Sciences, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Airport Bypass Road, Gandhi Nagar, Bhopal (MP)-462036, India
| | - Chandrabose Karthikeyan
- School of Pharmaceutical Sciences, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Airport Bypass Road, Gandhi Nagar, Bhopal (MP)-462036, India
| | - Shraddha V. Bhadada
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Amit K. Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - N.S. Hari Narayana Moorthy
- School of Pharmaceutical Sciences, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Airport Bypass Road, Gandhi Nagar, Bhopal (MP)-462036, India
| | - Piyush Trivedi
- School of Pharmaceutical Sciences, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Airport Bypass Road, Gandhi Nagar, Bhopal (MP)-462036, India
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B M, Manandhar S, Hari G, Priya K, Kumar B H, Pai KSR. Virtual structure-based docking, WaterMap, and molecular dynamics guided identification of the potential natural compounds as inhibitors of protein-tyrosine phosphatase 1B. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Maheshwari N, Karthikeyan C, Bhadada SV, Verma AK, Sahi C, Moorthy NHN, Trivedi P. Design, synthesis and biological evaluation of some tetrazole acetamide derivatives as novel non-carboxylic PTP1B inhibitors. Bioorg Chem 2019; 92:103221. [DOI: 10.1016/j.bioorg.2019.103221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/05/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022]
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Synthesis and biological evaluation of some N-(3-(1H-tetrazol-5-yl) phenyl)acetamide derivatives as novel non-carboxylic PTP1B inhibitors designed through bioisosteric modulation. Bioorg Chem 2018; 80:145-150. [DOI: 10.1016/j.bioorg.2018.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 12/11/2022]
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Khan MF, Rawat AK, Khatoon S, Hussain MK, Mishra A, Negi DS. In vitro and in vivo antidiabetic effect of extracts of Melia azedarach, Zanthoxylum alatum, and Tanacetum nubigenum. Integr Med Res 2018; 7:176-183. [PMID: 29984178 PMCID: PMC6026355 DOI: 10.1016/j.imr.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND To investigate the antidiabetic effect of Himalayan Medicinal plants from India viz. Melia azedarach (Family: Meliaceae), Zanthoxylum alatum (Family: Rutaceae), Tanacetum nubigenum (Family: Asteraceae) using in-vitro as well as in-vivo approaches. METHODS Their effects were examined on stimulation of glucose uptake by C2C12 cultured cell line, inhibitory effect on human recombinant Protein tyrosine phosphatase-1B (PTP-1B) and followed by the hypoglycaemic activity of extracts in Streptozotocin (STZ) induced diabetic rats. RESULTS All prepared extracts had been found to enrich with polyphenolic, flavonoids, terpenoids, anthraquinones and saponins type of compounds. n-Butanol fraction of Zanthoxylum alatum showed maximum PTP-1B inhibition (61.9%) whereas ethanol extract of Tanacetum nubigenum showed strong stimulation of glucose uptake (+61.2%) in C2Cl2 myotubes. In STZ induced Sprague-Dawley rats, significant decrease in blood glucose level was observed in ethanol extract of Melia azaderach treated group as 14.8% (p < 0.01) whereas in the ethanol extract of Tanacetum nubigenum treated group, it was observed as 15.5% (p < 0.01) compare to metformin which showed 26.8% (p < 0.01) lowering of blood glucose in the same time duration of 5 h study. CONCLUSION This study demonstrated that these plants have a significant therapeutic value in type-2-diabetes mellitus and related complications thus supporting their traditional uses in Indian traditional system of medicine.
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Affiliation(s)
- Mohammad Faheem Khan
- Department of Biotechnology, Era's Lucknow Medical College & Hospital, Era University, Lucknow, India
| | - Arun Kumar Rawat
- Biochemistry Division, CSIR-Central Drug Research Institute, CSIR, Lucknow, India
| | | | | | - Arvind Mishra
- Biochemistry Division, CSIR-Central Drug Research Institute, CSIR, Lucknow, India
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Sarabia-Sánchez MJ, Trejo-Soto PJ, Velázquez-López JM, Carvente-García C, Castillo R, Hernández-Campos A, Avitia-Domínguez C, Enríquez-Mendiola D, Sierra-Campos E, Valdez-Solana M, Salas-Pacheco JM, Téllez-Valencia A. Novel Mixed-Type Inhibitors of Protein Tyrosine Phosphatase 1B. Kinetic and Computational Studies. Molecules 2017; 22:molecules22122262. [PMID: 29261102 PMCID: PMC6150025 DOI: 10.3390/molecules22122262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 11/21/2022] Open
Abstract
The Atlas of Diabetes reports 415 million diabetics in the world, a number that has surpassed in half the expected time the twenty year projection. Type 2 diabetes is the most frequent form of the disease; it is characterized by a defect in the secretion of insulin and a resistance in its target organs. In the search for new antidiabetic drugs, one of the principal strategies consists in promoting the action of insulin. In this sense, attention has been centered in the protein tyrosine phosphatase 1B (PTP1B), a protein whose overexpression or increase of its activity has been related in many studies with insulin resistance. In the present work, a chemical library of 250 compounds was evaluated to determine their inhibition capability on the protein PTP1B. Ten molecules inhibited over the 50% of the activity of the PTP1B, the three most potent molecules were selected for its characterization, reporting Ki values of 5.2, 4.2 and 41.3 µM, for compounds 1, 2, and 3, respectively. Docking and molecular dynamics studies revealed that the three inhibitors made interactions with residues at the secondary binding site to phosphate, exclusive for PTP1B. The data reported here support these compounds as hits for the design more potent and selective inhibitors against PTP1B in the search of new antidiabetic treatment.
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Affiliation(s)
- Marie Jazmín Sarabia-Sánchez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
| | - Pedro Josué Trejo-Soto
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - José Miguel Velázquez-López
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Carlos Carvente-García
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Rafael Castillo
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Alicia Hernández-Campos
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
| | - Daniel Enríquez-Mendiola
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango C.P. 35010, Mexico.
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango C.P. 35010, Mexico.
| | - José Manuel Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Av. Universidad S/N, Durango, Durango C.P. 34000, Mexico.
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitúa S/N, Durango, Durango C.P. 34000, Mexico.
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Sepehri B, Ghavami R. The identification of new ATAD2 bromodomain inhibitors: the application of combined ligand and structure-based virtual screening. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:957-971. [PMID: 29191061 DOI: 10.1080/1062936x.2017.1385532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) approaches were used to identify new inhibitors for ATAD2 bromodomain. The LBVS approach was used to search 23,129,083 clean compounds to identify compounds similar to an active compound with reported pIC50 equal to 7.2. Based on LBVS results, 19 compounds were selected. To perform SBVS, by applying nine filters on 23,129,083 clean compounds, 1,057,060 compounds were selected. After performing SBVS on these selected compounds with idock software, 16 compounds with the lowest binding energies were selected. More accurate molecular docking analysis was performed on these 35 selected compounds by using iGEMDOCK software and six of them with the lowest binding energies were selected as hit compounds. These compounds were zinc36647229, zinc77969074, zinc13637358, zinc77971540, zinc12991296 and zinc19374204.
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Affiliation(s)
- B Sepehri
- a Department of Chemistry, Faculty of Science , University of Kurdistan , Sanandaj , Iran
| | - R Ghavami
- a Department of Chemistry, Faculty of Science , University of Kurdistan , Sanandaj , Iran
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Design, synthesis and molecular modelling studies of novel 3-acetamido-4-methyl benzoic acid derivatives as inhibitors of protein tyrosine phosphatase 1B. Eur J Med Chem 2013; 70:469-76. [DOI: 10.1016/j.ejmech.2013.10.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/20/2022]
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Molecular modeling and synthesis of ZINC02765569 derivatives as protein tyrosine phosphatase 1B inhibitors: lead optimization study. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0165-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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