1
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Skeens E, Maschietto F, Manjula R, Shillingford S, Lolis EJ, Batista VS, Bennett AM, Lisi GP. Dynamic and structural insights into allosteric regulation on MKP5 a dual-specificity phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611520. [PMID: 39282375 PMCID: PMC11398491 DOI: 10.1101/2024.09.05.611520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Dual-specificity mitogen-activated protein kinase (MAPK) phosphatases (MKPs) directly dephosphorylate and inactivate the MAPKs. Although the catalytic mechanism of dephosphorylation of the MAPKs by the MKPs is established, a complete molecular picture of the regulatory interplay between the MAPKs and MKPs still remains to be fully explored. Here, we sought to define the molecular mechanism of MKP5 regulation through an allosteric site within its catalytic domain. We demonstrate using crystallographic and NMR spectroscopy approaches that residue Y435 is required to maintain the structural integrity of the allosteric pocket. Along with molecular dynamics simulations, these data provide insight into how changes in the allosteric pocket propagate conformational flexibility in the surrounding loops to reorganize catalytically crucial residues in the active site. Furthermore, Y435 contributes to the interaction with p38 MAPK and JNK, thereby promoting dephosphorylation. Collectively, these results highlight the role of Y435 in the allosteric site as a novel mode of MKP5 regulation by p38 MAPK and JNK.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | | | - Ramu Manjula
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shanelle Shillingford
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elias J Lolis
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Anton M Bennett
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, Connecticut, USA
| | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
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2
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Cobley JN. Exploring the unmapped cysteine redox proteoform landscape. Am J Physiol Cell Physiol 2024; 327:C844-C866. [PMID: 39099422 DOI: 10.1152/ajpcell.00152.2024] [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: 03/07/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
Cysteine redox proteoforms define the diverse molecular states that proteins with cysteine residues can adopt. A protein with one cysteine residue must adopt one of two binary proteoforms: reduced or oxidized. Their numbers scale: a protein with 10 cysteine residues must assume one of 1,024 proteoforms. Although they play pivotal biological roles, the vast cysteine redox proteoform landscape comprising vast numbers of theoretical proteoforms remains largely uncharted. Progress is hampered by a general underappreciation of cysteine redox proteoforms, their intricate complexity, and the formidable challenges that they pose to existing methods. The present review advances cysteine redox proteoform theory, scrutinizes methodological barriers, and elaborates innovative technologies for detecting unique residue-defined cysteine redox proteoforms. For example, chemistry-enabled hybrid approaches combining the strengths of top-down mass spectrometry (TD-MS) and bottom-up mass spectrometry (BU-MS) for systematically cataloguing cysteine redox proteoforms are delineated. These methods provide the technological means to map uncharted redox terrain. To unravel hidden redox regulatory mechanisms, discover new biomarkers, and pinpoint therapeutic targets by mining the theoretical cysteine redox proteoform space, a community-wide initiative termed the "Human Cysteine Redox Proteoform Project" is proposed. Exploring the cysteine redox proteoform landscape could transform current understanding of redox biology.
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Affiliation(s)
- James N Cobley
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
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3
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Sun Y, Dinenno FA, Tang P, Kontaridis MI. Protein tyrosine phosphatase 1B in metabolic and cardiovascular diseases: from mechanisms to therapeutics. Front Cardiovasc Med 2024; 11:1445739. [PMID: 39238503 PMCID: PMC11374623 DOI: 10.3389/fcvm.2024.1445739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024] Open
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) has emerged as a significant regulator of metabolic and cardiovascular disease. It is a non-transmembrane protein tyrosine phosphatase that negatively regulates multiple signaling pathways integral to the regulation of growth, survival, and differentiation of cells, including leptin and insulin signaling, which are critical for development of obesity, insulin resistance, type 2 diabetes, and cardiovascular disease. Given PTP1B's central role in glucose homeostasis, energy balance, and vascular function, targeted inhibition of PTP1B represents a promising strategy for treating these diseases. However, challenges, such as off-target effects, necessitate a focus on tissue-specific approaches, to maximize therapeutic benefits while minimizing adverse outcomes. In this review, we discuss molecular mechanisms by which PTP1B influences metabolic and cardiovascular functions, summarize the latest research on tissue-specific roles of PTP1B, and discuss the potential for PTP1B inhibitors as future therapeutic agents.
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Affiliation(s)
- Yan Sun
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, Utica, NY, United States
| | - Frank A Dinenno
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, Utica, NY, United States
| | - Peiyang Tang
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, Utica, NY, United States
| | - Maria I Kontaridis
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, Utica, NY, United States
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
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4
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Zhan J, Liu Z, Gao H. Theoretical study on the design of allosteric inhibitors of diabetes associated protein PTP1B. Front Pharmacol 2024; 15:1423029. [PMID: 39239651 PMCID: PMC11374740 DOI: 10.3389/fphar.2024.1423029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024] Open
Abstract
The protein tyrosine phosphatase 1B (PTP1B) is a critical therapeutic target for type 2 diabetes mellitus (T2DM). Many PTP1B inhibitors have been reported, however, most of them lack high specificity and have adverse effects. Designing effective PTP1B inhibitors requires understanding the molecular mechanism of action between inhibitors and PTP1B. To this end, molecular dynamics (MD) simulations and molecular mechanics Poisson Boltzmann Surface Area (MM-PB/SA) methods were used to observe the binding patterns of compounds with similar pentacyclic triterpene parent ring structures but different inhibition abilities. Through structure and energy analysis, we found that the positions of cavities and substituents significantly affect combining capacity. Besides, we constructed a series of potential inhibitor molecules using LUDI and rational drug design methods. The ADMET module of Discovery Studio 2020 was used to predict the properties of these inhibitor molecules. Lastly, we obtained compounds with low toxicity and significant inhibitory activity. The study will contribute to the treatment of T2DM.
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Affiliation(s)
- Jiuyu Zhan
- School of Life Science, Ludong University, Yantai, Shandong, China
| | - Zhenyang Liu
- School of Life Science, Ludong University, Yantai, Shandong, China
| | - Hongwei Gao
- School of Life Science, Ludong University, Yantai, Shandong, China
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5
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Perdikari A, Woods VA, Ebrahim A, Lawler K, Bounds R, Singh NI, Mehlman T(S, Riley BT, Sharma S, Morris JW, Keogh JM, Henning E, Smith M, Farooqi IS, Keedy DA. Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.603709. [PMID: 39149290 PMCID: PMC11326154 DOI: 10.1101/2024.08.05.603709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of leptin signaling whose disruption protects against diet-induced obesity in mice. We investigated whether structural characterization of human PTP1B variant proteins might reveal precise mechanisms to target for weight loss therapy. We selected 12 rare variants for functional characterization from exomes from 997 people with persistent thinness and 200,000 people from UK Biobank. Seven of 12 variants impaired PTP1B function by increasing leptin-stimulated STAT3 phosphorylation in cells. Using room-temperature X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, and computational modeling, we determined that human variants modulate the 3-dimensional structure of PTP1B through distinct allosteric conduits that energetically link distal, highly ligandable structural regions to the active site. These studies inform the design of allosteric PTP1B inhibitors for the treatment of obesity.
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Affiliation(s)
- Aliki Perdikari
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Virgil A. Woods
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center; New York, NY 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Katherine Lawler
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Rebecca Bounds
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Nathanael I. Singh
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Tamar (Skaist) Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center; New York, NY 10016, USA
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - 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
| | - Jackson W. Morris
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Julia M. Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - 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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6
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Coronell-Tovar A, Pardo JP, Rodríguez-Romero A, Sosa-Peinado A, Vásquez-Bochm L, Cano-Sánchez P, Álvarez-Añorve LI, González-Andrade M. Protein tyrosine phosphatase 1B (PTP1B) function, structure, and inhibition strategies to develop antidiabetic drugs. FEBS Lett 2024; 598:1811-1838. [PMID: 38724486 DOI: 10.1002/1873-3468.14901] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 08/13/2024]
Abstract
Tyrosine protein phosphatase non-receptor type 1 (PTP1B; also known as protein tyrosine phosphatase 1B) is a member of the protein tyrosine phosphatase (PTP) family and is a soluble enzyme that plays an essential role in different physiological processes, including the regulation of metabolism, specifically in insulin and leptin sensitivity. PTP1B is crucial in the pathogenesis of type 2 diabetes mellitus and obesity. These biological functions have made PTP1B validated as an antidiabetic and anti-obesity, and potentially anticancer, molecular target. Four main approaches aim to inhibit PTP1B: orthosteric, allosteric, bidentate inhibition, and PTPN1 gene silencing. Developing a potent and selective PTP1B inhibitor is still challenging due to the enzyme's ubiquitous expression, subcellular location, and structural properties. This article reviews the main advances in the study of PTP1B since it was first isolated in 1988, as well as recent contextual information related to the PTP family to which this protein belongs. Furthermore, we offer an overview of the role of PTP1B in diabetes and obesity, and the challenges to developing selective, effective, potent, bioavailable, and cell-permeable compounds that can inhibit the enzyme.
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Affiliation(s)
- Andrea Coronell-Tovar
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Juan P Pardo
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Alejandro Sosa-Peinado
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luz Vásquez-Bochm
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Patricia Cano-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Laura Iliana Álvarez-Añorve
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Martin González-Andrade
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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7
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Wang A, Zhang Y, Lv X, Liang G. Therapeutic potential of targeting protein tyrosine phosphatases in liver diseases. Acta Pharm Sin B 2024; 14:3295-3311. [PMID: 39220870 PMCID: PMC11365412 DOI: 10.1016/j.apsb.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 09/04/2024] Open
Abstract
Protein tyrosine phosphorylation is a post-translational modification that regulates protein structure to modulate demic organisms' homeostasis and function. This physiological process is regulated by two enzyme families, protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). As an important regulator of protein function, PTPs are indispensable for maintaining cell intrinsic physiology in different systems, as well as liver physiological and pathological processes. Dysregulation of PTPs has been implicated in multiple liver-related diseases, including chronic liver diseases (CLDs), hepatocellular carcinoma (HCC), and liver injury, and several PTPs are being studied as drug therapeutic targets. Therefore, given the regulatory role of PTPs in diverse liver diseases, a collated review of their function and mechanism is necessary. Moreover, based on the current research status of targeted therapy, we emphasize the inclusion of several PTP members that are clinically significant in the development and progression of liver diseases. As an emerging breakthrough direction in the treatment of liver diseases, this review summarizes the research status of PTP-targeting compounds in liver diseases to illustrate their potential in clinical treatment. Overall, this review aims to support the development of novel PTP-based treatment pathways for liver diseases.
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Affiliation(s)
- Ao Wang
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji 133002, China
| | - Yi Zhang
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
| | - Xinting Lv
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
| | - Guang Liang
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji 133002, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
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8
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Mendoza-Jasso ME, Pérez-Villanueva J, Alvarado-Rodríguez JG, González-Andrade M, Cortés-Benítez F. 3-Benzylaminomethyl Lithocholic Acid Derivatives Exhibited Potent and Selective Uncompetitive Inhibitory Activity Against Protein Tyrosine Phosphatase 1B (PTP1B). ACS OMEGA 2024; 9:33224-33238. [PMID: 39100322 PMCID: PMC11292843 DOI: 10.1021/acsomega.4c04948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/21/2024] [Accepted: 07/09/2024] [Indexed: 08/06/2024]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a promising drug target for treating type 2 diabetes (T2DM) and obesity. As a result, developing new therapies that target PTP1B is an attractive strategy for treating these diseases. Herein, we detail the synthesis of 15 lithocholic acid (LA) derivatives, each containing different benzylaminomethyl groups attached to the C3 position of the steroid skeleton. The derivatives were assessed against two forms of PTP1B enzyme (hPTP1B1-400 and hPTP1B1-285), and the most potent compounds were then tested against T-cell protein tyrosine phosphatase (TCPTP) to determine their selectivity. The results showed that compounds 6m and 6n were more potent than the reference compounds (ursolic acid, chlorogenic acid, suramin, and TCS401). Additionally, both compounds exhibited greater potency over hPTP1B1-400. Furthermore, enzyme kinetic studies on hPTP1B1-400 revealed that these two lithocholic acid derivatives have an uncompetitive inhibition against hPTP1B1-400 with K i values of 2.5 and 3.4 μM, respectively. Interestingly, these compounds were around 75-fold more selective for PTP1B over TCPTP. Finally, docking studies and molecular dynamics simulations (MDS) were conducted to determine how these compounds interact with PTP1B. The docking studies revealed hydrophobic and H-bond interactions with amino acid residues in the unstructured region. MDS showed that these interactions persisted throughout the 200 ns simulation, indicating the crucial role of the unstructured zone in the biological activity and inhibition of PTP1B.
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Affiliation(s)
- María-Eugenia Mendoza-Jasso
- Doctorado
en Ciencias Farmacéuticas, División de Ciencias Biológicas
y de la Salud, Universidad Autónoma
Metropolitana − Unidad Xochimilco, Ciudad de México 04960, Mexico
- Laboratorio
de Síntesis y Aislamiento de Sustancias Bioactivas, Departamento
de Sistemas Biológicos, División de Ciencias Biológicas
y de la Salud, Universidad Autónoma
Metropolitana − Unidad Xochimilco, Ciudad de México 04960, Mexico
- Laboratorio
de Biosensores y Modelaje Molecular, Departamento de Bioquímica,
Facultad de Medicina, Universidad Nacional
Autónoma de México, Ciudad de México 04510, Mexico
| | - Jaime Pérez-Villanueva
- Laboratorio
de Síntesis y Aislamiento de Sustancias Bioactivas, Departamento
de Sistemas Biológicos, División de Ciencias Biológicas
y de la Salud, Universidad Autónoma
Metropolitana − Unidad Xochimilco, Ciudad de México 04960, Mexico
| | | | - Martin González-Andrade
- Laboratorio
de Biosensores y Modelaje Molecular, Departamento de Bioquímica,
Facultad de Medicina, Universidad Nacional
Autónoma de México, Ciudad de México 04510, Mexico
| | - Francisco Cortés-Benítez
- Laboratorio
de Síntesis y Aislamiento de Sustancias Bioactivas, Departamento
de Sistemas Biológicos, División de Ciencias Biológicas
y de la Salud, Universidad Autónoma
Metropolitana − Unidad Xochimilco, Ciudad de México 04960, Mexico
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9
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Saeed AA, Klureza MA, Hekstra DR. Mapping protein conformational landscapes from crystallographic drug fragment screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605395. [PMID: 39131376 PMCID: PMC11312500 DOI: 10.1101/2024.07.29.605395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Proteins are dynamic macromolecules. Knowledge of a protein's thermally accessible conformations is critical to determining important transitions and designing therapeutics. Accessible conformations are highly constrained by a protein's structure such that concerted structural changes due to external perturbations likely track intrinsic conformational transitions. These transitions can be thought of as paths through a conformational landscape. Crystallographic drug fragment screens are high-throughput perturbation experiments, in which thousands of crystals of a drug target are soaked with small-molecule drug precursors (fragments) and examined for fragment binding, mapping potential drug binding sites on the target protein. Here, we describe an open-source Python package, COLAV (COnformational LAndscape Visualization), to infer conformational landscapes from such large-scale crystallographic perturbation studies. We apply COLAV to drug fragment screens of two medically important systems: protein tyrosine phosphatase 1B (PTP-1B), which regulates insulin signaling, and the SARS CoV-2 Main Protease (MPro). With enough fragment-bound structures, we find that such drug screens also enable detailed mapping of proteins' conformational landscapes.
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Affiliation(s)
- Ammaar A. Saeed
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Margaret A. Klureza
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Doeke R. Hekstra
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA 02138
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10
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Chartier CA, Woods VA, Xu Y, van Vlimmeren AE, Jovanovic M, McDermott AE, Keedy DA, Shah NH. Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603632. [PMID: 39071364 PMCID: PMC11275736 DOI: 10.1101/2024.07.16.603632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The rapid identification of protein-protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and proximity-labeling proteomics. While these methods can reveal networks of interacting proteins, they cannot reveal how specific protein-protein interactions alter cell signaling or protein function. For instance, when two proteins interact, there can be emergent signaling processes driven purely by the individual activities of those proteins being co-localized. Alternatively, protein-protein interactions can allosterically regulate function, enhancing or suppressing activity in response to binding. In this work, we investigate the interaction between the tyrosine phosphatase PTP1B and the adaptor protein Grb2, which have been annotated as binding partners in a number of proteomics studies. This interaction has been postulated to co-localize PTP1B with its substrate IRS-1 by forming a ternary complex, thereby enhancing the dephosphorylation of IRS-1 to suppress insulin signaling. Here, we report that Grb2 binding to PTP1B also allosterically enhances PTP1B catalytic activity. We show that this interaction is dependent on the proline-rich region of PTP1B, which interacts with the C-terminal SH3 domain of Grb2. Using NMR spectroscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) we show that Grb2 binding alters PTP1B structure and/or dynamics. Finally, we use MS proteomics to identify other interactors of the PTP1B proline-rich region that may also regulate PTP1B function similarly to Grb2. This work presents one of the first examples of a protein allosterically regulating the enzymatic activity of PTP1B and lays the foundation for discovering new mechanisms of PTP1B regulation in cell signaling. Significance Statement Protein-protein interactions are critical for cell signaling. The interaction between the phosphatase PTP1B and adaptor protein Grb2 co-localizes PTP1B with its substrates, thereby enhancing their dephosphorylation. We show that Grb2 binding also directly modulates PTP1B activity through an allosteric mechanism involving the proline-rich region of PTP1B. Our study reveals a novel mode of PTP1B regulation through a protein-protein interaction that is likely to be exploited by other cellular interactors of this important signaling enzyme.
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11
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Zhou Y, Yao Z, Lin Y, Zhang H. From Tyrosine Kinases to Tyrosine Phosphatases: New Therapeutic Targets in Cancers and Beyond. Pharmaceutics 2024; 16:888. [PMID: 39065585 PMCID: PMC11279542 DOI: 10.3390/pharmaceutics16070888] [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: 04/25/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) regulate the level of tyrosine phosphorylation in proteins. PTKs are key enzymes that catalyze the transfer of an ATP phosphoric acid to a tyrosine residue on target protein substrates. Protein tyrosine phosphatases (PTPs) are responsible for the dephosphorylation of tyrosine residues and play a role in countering PTK overactivity. As widespread oncogenes, PTKs were once considered to be promising targets for therapy. However, tyrosine kinase inhibitors (TKIs) now face a number of challenges, including drug resistance and toxic side effects. Treatment strategies now need to be developed from a new perspective. In this review, we assess the current state of TKIs and highlight the role of PTPs in cancer and other diseases. With the advances of allosteric inhibition and the development of multiple alternative proprietary drug strategies, the reputation of PTPs as "undruggable" targets has been overturned, and they are now considered viable therapeutic targets. We also discuss the strategies and prospects of PTP-targeted therapy, as well as its future development.
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Affiliation(s)
- Yu Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
| | - Zhimeng Yao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Urology Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510660, China
| | - Yusheng Lin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510660, China
| | - Hao Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Pathology, Gongli Hospital of Shanghai Pudong New Area, Shanghai 200135, China
- Zhuhai Institute of Jinan University, Zhuhai 511436, China
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12
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Gong B, Johnston JD, Thiemicke A, de Marco A, Meyer T. Endoplasmic reticulum-plasma membrane contact gradients direct cell migration. Nature 2024; 631:415-423. [PMID: 38867038 PMCID: PMC11236710 DOI: 10.1038/s41586-024-07527-5] [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: 03/22/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Directed cell migration is driven by the front-back polarization of intracellular signalling1-3. Receptor tyrosine kinases and other inputs activate local signals that trigger membrane protrusions at the front2,4-6. Equally important is a long-range inhibitory mechanism that suppresses signalling at the back to prevent the formation of multiple fronts7-9. However, the identity of this mechanism is unknown. Here we report that endoplasmic reticulum-plasma membrane (ER-PM) contact sites are polarized in single and collectively migrating cells. The increased density of these ER-PM contacts at the back provides the ER-resident PTP1B phosphatase more access to PM substrates, which confines receptor signalling to the front and directs cell migration. Polarization of the ER-PM contacts is due to microtubule-regulated polarization of the ER, with more RTN4-rich curved ER at the front and more CLIMP63-rich flattened ER at the back. The resulting ER curvature gradient leads to small and unstable ER-PM contacts only at the front. These contacts flow backwards and grow to large and stable contacts at the back to form the front-back ER-PM contact gradient. Together, our study suggests that the structural polarity mediated by ER-PM contact gradients polarizes cell signalling, directs cell migration and prolongs cell migration.
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Affiliation(s)
- Bo Gong
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
| | - Jake D Johnston
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alexander Thiemicke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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13
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Kołodziej-Sobczak D, Sobczak Ł, Łączkowski KZ. Protein Tyrosine Phosphatase 1B (PTP1B): A Comprehensive Review of Its Role in Pathogenesis of Human Diseases. Int J Mol Sci 2024; 25:7033. [PMID: 39000142 PMCID: PMC11241624 DOI: 10.3390/ijms25137033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Overexpression of protein tyrosine phosphatase 1B (PTP1B) disrupts signaling pathways and results in numerous human diseases. In particular, its involvement has been well documented in the pathogenesis of metabolic disorders (diabetes mellitus type I and type II, fatty liver disease, and obesity); neurodegenerative diseases (Alzheimer's disease, Parkinson's disease); major depressive disorder; calcific aortic valve disease; as well as several cancer types. Given this multitude of therapeutic applications, shortly after identification of PTP1B and its role, the pursuit to introduce safe and selective enzyme inhibitors began. Regrettably, efforts undertaken so far have proved unsuccessful, since all proposed PTP1B inhibitors failed, or are yet to complete, clinical trials. Intending to aid introduction of the new generation of PTP1B inhibitors, this work collects and organizes the current state of the art. In particular, this review intends to elucidate intricate relations between numerous diseases associated with the overexpression of PTP1B, as we believe that it is of the utmost significance to establish and follow a brand-new holistic approach in the treatment of interconnected conditions. With this in mind, this comprehensive review aims to validate the PTP1B enzyme as a promising molecular target, and to reinforce future research in this direction.
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Affiliation(s)
- Dominika Kołodziej-Sobczak
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland;
| | - Łukasz Sobczak
- Hospital Pharmacy, Multidisciplinary Municipal Hospital in Bydgoszcz, Szpitalna 19, 85-826 Bydgoszcz, Poland
| | - Krzysztof Z. Łączkowski
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland;
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14
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Dong J, Jassim BA, Milholland KL, Qu Z, Bai Y, Miao Y, Miao J, Ma Y, Lin J, Hall MC, Zhang ZY. Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases. J Med Chem 2024; 67:8817-8835. [PMID: 38768084 DOI: 10.1021/acs.jmedchem.4c00149] [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: 05/22/2024]
Abstract
Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) control protein tyrosine phosphorylation and regulate numerous cellular functions. Dysregulated PTP activity is associated with the onset of multiple human diseases. Nevertheless, understanding of the physiological function and disease biology of most PTPs remains limited, largely due to the lack of PTP-specific chemical probes. In this study, starting from a well-known nonhydrolyzable phosphotyrosine (pTyr) mimetic, phosphonodifluoromethyl phenylalanine (F2Pmp), we synthesized 7 novel phosphonodifluoromethyl-containing bicyclic/tricyclic aryl derivatives with improved cell permeability and potency toward various PTPs. Furthermore, with fragment- and structure-based design strategies, we advanced compound 9 to compound 15, a first-in-class, potent, selective, and bioavailable inhibitor of human CDC14A and B phosphatases. This study demonstrates the applicability of the fragment-based design strategy in creating potent, selective, and bioavailable PTP inhibitors and provides a valuable probe for interrogating the biological roles of hCDC14 phosphatases and assessing their potential for therapeutic interventions.
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Affiliation(s)
- Jiajun Dong
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brenson A Jassim
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yunpeng Bai
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yiming Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuan Ma
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianping Lin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
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15
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Zhuang C, Yang S, Gonzalez CG, Ainsworth RI, Li S, Kobayashi MT, Wierzbicki I, Rossitto LAM, Wen Y, Peti W, Stanford SM, Gonzalez DJ, Murali R, Santelli E, Bottini N. A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling. J Biol Chem 2024; 300:107393. [PMID: 38777143 PMCID: PMC11237943 DOI: 10.1016/j.jbc.2024.107393] [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: 02/22/2024] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 posttranslational regulation. Here, we characterize a phosphorylation site at Ser325 situated C terminal to the catalytic domain of PTPN22 and its roles in altering protein function. In human T cells, Ser325 is phosphorylated by glycogen synthase kinase-3 (GSK3) following TCR stimulation, which promotes its TCR-inhibitory activity. Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9-mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Global phospho-mass spectrometry showed Ser325 phosphorylation state alters downstream transcriptional activity through enrichment of Swi3p, Rsc8p, and Moira domain binding proteins, and next-generation sequencing revealed it differentially regulates the expression of chemokines and T cell activation pathways. Moreover, in vitro kinetic data suggest the modulation of activity depends on a cellular context. Finally, we begin to address the structural and mechanistic basis for the influence of Ser325 phosphorylation on the protein's properties by deuterium exchange mass spectrometry and NMR spectroscopy. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling and provides details that might inform the future development of allosteric modulators of PTPN22.
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Affiliation(s)
- Chuling Zhuang
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - Shen Yang
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carlos G Gonzalez
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Richard I Ainsworth
- Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, California, USA
| | - Masumi Takayama Kobayashi
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Igor Wierzbicki
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Leigh-Ana M Rossitto
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Yutao Wen
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Stephanie M Stanford
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eugenio Santelli
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nunzio Bottini
- Department of Medicine, Altman Clinical and Translational Research Institute, University of California, San Diego, California, USA; Department of Medicine, Kao Autoimmunity Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.
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16
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Delibegović M, Dall'Angelo S, Dekeryte R. Protein tyrosine phosphatase 1B in metabolic diseases and drug development. Nat Rev Endocrinol 2024; 20:366-378. [PMID: 38519567 DOI: 10.1038/s41574-024-00965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/25/2024]
Abstract
Protein tyrosine phosphatase 1B (PTP1B), a non-transmembrane phosphatase, has a major role in a variety of signalling pathways, including direct negative regulation of classic insulin and leptin signalling pathways, and is implicated in the pathogenesis of several cardiometabolic diseases and cancers. As such, PTP1B has been a therapeutic target for over two decades, with PTP1B inhibitors identified either from natural sources or developed throughout the years. Some of these inhibitors have reached phase I and/or II clinical trials in humans for the treatment of type 2 diabetes mellitus, obesity and/or metastatic breast cancer. In this Review, we summarize the cellular processes and regulation of PTP1B, discuss evidence from in vivo preclinical and human studies of the association between PTP1B and different disorders, and discuss outcomes of clinical trials. We outline challenges associated with the targeting of this phosphatase (which was, until the past few years, viewed as difficult to target), the current state of the field of PTP1B inhibitors (and dual phosphatase inhibitors) and future directions for manipulating the activity of this key metabolic enzyme.
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Affiliation(s)
- Mirela Delibegović
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK.
| | - Sergio Dall'Angelo
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
| | - Ruta Dekeryte
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
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17
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Woods VA, Abzalimov RR, Keedy DA. Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS. Protein Sci 2024; 33:e5024. [PMID: 38801229 PMCID: PMC11129624 DOI: 10.1002/pro.5024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/27/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for obesity, diabetes, and certain types of cancer. In particular, allosteric inhibitors hold potential for therapeutic use, but an incomplete understanding of conformational dynamics and allostery in this protein has hindered their development. Here, we interrogate solution dynamics and allosteric responses in PTP1B using high-resolution hydrogen-deuterium exchange mass spectrometry (HDX-MS), an emerging and powerful biophysical technique. Using HDX-MS, we obtain a detailed map of backbone amide exchange that serves as a proxy for the solution dynamics of apo PTP1B, revealing several flexible loops interspersed among more constrained and rigid regions within the protein structure, as well as local regions that exchange faster than expected from their secondary structure and solvent accessibility. We demonstrate that our HDX rate data obtained in solution adds value to estimates of conformational heterogeneity derived from a pseudo-ensemble constructed from ~200 crystal structures of PTP1B. Furthermore, we report HDX-MS maps for PTP1B with active-site versus allosteric small-molecule inhibitors. These maps suggest distinct and widespread effects on protein dynamics relative to the apo form, including changes in locations distal (>35 Å) from the respective ligand binding sites. These results illuminate that allosteric inhibitors of PTP1B can induce unexpected changes in dynamics that extend beyond the previously understood allosteric network. Together, our data suggest a model of BB3 allostery in PTP1B that combines conformational restriction of active-site residues with compensatory liberation of distal residues that aid in entropic balancing. Overall, our work showcases the potential of HDX-MS for elucidating aspects of protein conformational dynamics and allosteric effects of small-molecule ligands and highlights the potential of integrating HDX-MS alongside other complementary methods, such as room-temperature X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations, to guide the development of new therapeutics.
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Affiliation(s)
- Virgil A. Woods
- Structural Biology InitiativeCUNY Advanced Science Research CenterNew YorkNew YorkUSA
- PhD Program in BiochemistryCUNY Graduate CenterNew YorkNew YorkUSA
| | - Rinat R. Abzalimov
- Structural Biology InitiativeCUNY Advanced Science Research CenterNew YorkNew YorkUSA
| | - Daniel A. Keedy
- Structural Biology InitiativeCUNY Advanced Science Research CenterNew YorkNew YorkUSA
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkNew YorkUSA
- PhD Programs in Biochemistry, Biology, & ChemistryCUNY Graduate CenterNew YorkNew YorkUSA
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18
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Rezhdo A, Hershman RL, Van Deventer JA. Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596443. [PMID: 38853888 PMCID: PMC11160716 DOI: 10.1101/2024.05.29.596443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In vitro display technologies, exemplified by phage and yeast display, have emerged as powerful platforms for antibody discovery and engineering. However, the identification of antibodies that disrupt target functions beyond binding remains a challenge. In particular, there are very few strategies that support identification and engineering of either protein-based irreversible binders or inhibitory enzyme binders. Expanding the range of chemistries in antibody libraries has the potential to lead to efficient discovery of function-disrupting antibodies. In this work, we describe a yeast display-based platform for the discovery of chemically diversified antibodies. We constructed a billion-member antibody library that supports the presentation of a range of chemistries within antibody variable domains via noncanonical amino acid (ncAA) incorporation and subsequent bioorthogonal click chemistry conjugations. Use of a polyspecific orthogonal translation system enables introduction of chemical groups with various properties, including photo-reactive, proximity-reactive, and click chemistry-enabled functional groups for library screening. We established conjugation conditions that facilitate modification of the full library, demonstrating the feasibility of sorting the full billion-member library in "protein-small molecule hybrid" format in future work. Here, we conducted initial library screens after introducing O-(2-bromoethyl)tyrosine (OBeY), a weakly electrophilic ncAA capable of undergoing proximity-induced crosslinking to a target. Enrichments against donkey IgG and protein tyrosine phosphatase 1B (PTP1B) each led to the identification of several OBeY-substituted clones that bind to the targets of interest. Flow cytometry analysis on the yeast surface confirmed higher retention of binding for OBeY-substituted clones compared to clones substituted with ncAAs lacking electrophilic side chains after denaturation. However, subsequent crosslinking experiments in solution with ncAA-substituted clones yielded inconclusive results, suggesting that weakly reactive OBeY side chain is not sufficient to drive robust crosslinking in the clones isolated here. Nonetheless, this work establishes a multi-modal, chemically expanded antibody library and demonstrates the feasibility of conducting discovery campaigns in chemically expanded format. This versatile platform offers new opportunities for identifying and characterizing antibodies with properties beyond what is accessible with the canonical amino acids, potentially enabling discovery of new classes of reagents, diagnostics, and even therapeutic leads.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Rebecca L Hershman
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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19
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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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20
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Perez-Quintero LA, Abidin BM, Tremblay ML. Immunotherapeutic implications of negative regulation by protein tyrosine phosphatases in T cells: the emerging cases of PTP1B and TCPTP. Front Med (Lausanne) 2024; 11:1364778. [PMID: 38707187 PMCID: PMC11066278 DOI: 10.3389/fmed.2024.1364778] [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: 01/03/2024] [Accepted: 03/27/2024] [Indexed: 05/07/2024] Open
Abstract
In the context of inflammation, T cell activation occurs by the concerted signals of the T cell receptor (TCR), co-stimulatory receptors ligation, and a pro-inflammatory cytokine microenvironment. Fine-tuning these signals is crucial to maintain T cell homeostasis and prevent self-reactivity while offering protection against infectious diseases and cancer. Recent developments in understanding the complex crosstalk between the molecular events controlling T cell activation and the balancing regulatory cues offer novel approaches for the development of T cell-based immunotherapies. Among the complex regulatory processes, the balance between protein tyrosine kinases (PTK) and the protein tyrosine phosphatases (PTPs) controls the transcriptional and metabolic programs that determine T cell function, fate decision, and activation. In those, PTPs are de facto regulators of signaling in T cells acting for the most part as negative regulators of the canonical TCR pathway, costimulatory molecules such as CD28, and cytokine signaling. In this review, we examine the function of two close PTP homologs, PTP1B (PTPN1) and T-cell PTP (TCPTP; PTPN2), which have been recently identified as promising candidates for novel T-cell immunotherapeutic approaches. Herein, we focus on recent studies that examine the known contributions of these PTPs to T-cell development, homeostasis, and T-cell-mediated immunity. Additionally, we describe the signaling networks that underscored the ability of TCPTP and PTP1B, either individually and notably in combination, to attenuate TCR and JAK/STAT signals affecting T cell responses. Thus, we anticipate that uncovering the role of these two PTPs in T-cell biology may lead to new treatment strategies in the field of cancer immunotherapy. This review concludes by exploring the impacts and risks that pharmacological inhibition of these PTP enzymes offers as a therapeutic approach in T-cell-based immunotherapies.
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Affiliation(s)
- Luis Alberto Perez-Quintero
- Rosalind and Morris Goodman Cancer Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Belma Melda Abidin
- Rosalind and Morris Goodman Cancer Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Michel L. Tremblay
- Rosalind and Morris Goodman Cancer Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
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21
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Chen L, Qian Z, Zheng Y, Zhang J, Sun J, Zhou C, Xiao H. Structural analysis of PTPN21 reveals a dominant-negative effect of the FERM domain on its phosphatase activity. SCIENCE ADVANCES 2024; 10:eadi7404. [PMID: 38416831 PMCID: PMC10901363 DOI: 10.1126/sciadv.adi7404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/24/2024] [Indexed: 03/01/2024]
Abstract
PTPN21 belongs to the four-point-one, ezrin, radixin, moesin (FERM) domain-containing protein tyrosine phosphatases (PTP) and plays important roles in cytoskeleton-associated cellular processes like cell adhesion, motility, and cargo transport. Because of the presence of a WPE loop instead of a WPD loop in the phosphatase domain, it is often considered to lack phosphatase activity. However, many of PTPN21's biological functions require its catalytic activity. To reconcile these findings, we have determined the structures of individual PTPN21 FERM, PTP domains, and a complex between FERM-PTP. Combined with biochemical analysis, we have found that PTPN21 PTP is weakly active and is autoinhibited by association with its FERM domain. Disruption of FERM-PTP interaction results in enhanced ERK activation. The oncogenic HPV18 E7 protein binds to PTP at the same location as PTPN21 FERM, indicating that it may act by displacing the FERM domain from PTP. Our results provide mechanistic insight into PTPN21 and benefit functional studies of PTPN21-mediated processes.
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Affiliation(s)
- Lu Chen
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zijun Qian
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yuyuan Zheng
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Zhang
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Jie Sun
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chun Zhou
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Haowen Xiao
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
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22
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Salmond RJ. Targeting Protein Tyrosine Phosphatases to Improve Cancer Immunotherapies. Cells 2024; 13:231. [PMID: 38334623 PMCID: PMC10854786 DOI: 10.3390/cells13030231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Advances in immunotherapy have brought significant therapeutic benefits to many cancer patients. Nonetheless, many cancer types are refractory to current immunotherapeutic approaches, meaning that further targets are required to increase the number of patients who benefit from these technologies. Protein tyrosine phosphatases (PTPs) have long been recognised to play a vital role in the regulation of cancer cell biology and the immune response. In this review, we summarize the evidence for both the pro-tumorigenic and tumour-suppressor function of non-receptor PTPs in cancer cells and discuss recent data showing that several of these enzymes act as intracellular immune checkpoints that suppress effective tumour immunity. We highlight new data showing that the deletion of inhibitory PTPs is a rational approach to improve the outcomes of adoptive T cell-based cancer immunotherapies and describe recent progress in the development of PTP inhibitors as anti-cancer drugs.
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Affiliation(s)
- Robert J Salmond
- Leeds Institute of Medical Research at St. James's, School of Medicine, University of Leeds, Leeds LS9 7TF, UK
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23
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Qu Z, Dong J, Zhang ZY. Protein tyrosine phosphatases as emerging targets for cancer immunotherapy. Br J Pharmacol 2023:10.1111/bph.16304. [PMID: 38116815 PMCID: PMC11186978 DOI: 10.1111/bph.16304] [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: 08/30/2023] [Revised: 11/03/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
Contemporary strategies in cancer immunotherapy, despite remarkable success, remain constrained by inherent limitations such as suboptimal patient responses, the emergence of drug resistance, and the manifestation of pronounced adverse effects. Consequently, the need for alternative strategies for immunotherapy becomes clear. Protein tyrosine phosphatases (PTPs) wield a pivotal regulatory influence over an array of essential cellular processes. Substantial research has underscored the potential in targeting PTPs to modulate the immune responses and/or regulate antigen presentation, thereby presenting a novel paradigm for cancer immunotherapy. In this review, we focus on recent advances in genetic and biological validation of several PTPs as emerging targets for immunotherapy. We also highlight recent development of small molecule inhibitors and degraders targeting these PTPs as novel cancer immunotherapeutic agents.
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Affiliation(s)
- Zihan Qu
- Department of Chemistry, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Jiajun Dong
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
- Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
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24
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Aguilar-Ramírez E, Reyes-Pérez V, Fajardo-Hernández CA, Quezada-Suaste CD, Carreón-Escalante M, Merlin-Lucas V, Quiroz-García B, Granados-Soto V, Rivera-Chávez J. Harnessing the Reactivity of Duclauxin toward Obtaining hPTP1B 1-400 Inhibitors. J Med Chem 2023; 66:16222-16234. [PMID: 38051546 DOI: 10.1021/acs.jmedchem.3c01594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Duclauxin (1) from Talaromyces sp. IQ-313 was reported as a putative allosteric modulator of human recombinant protein tyrosine phosphatase 1B (400 amino acids) (hPTP1B1-400), a validated target for the treatment of type II diabetes. Based on these findings, a one-strain-many-compound (OSMAC) experiment on the IQ-313 strain generated derivatives 5a, 6, and 7. Moreover, a one-/two-step semisynthetic approach guided by docking toward hPTP1B1-400 produced 38 analogs, a series (A) incorporating a lactam functionalization at C-1 (8a-15a, 36a, and 37a) and a series (B) containing a lactam at C-1 and an extra unsaturation between C-7 and C-8 (5b, 11b-37b). In vitro evaluation and structure-activity relationship (SAR) analysis revealed that analogs from the B series are up to 10-fold more active than 1 and derivatives from the A series. Furthermore, duclauxin (1) and 36b were assessed for their potential acute toxicity, estimating their LD50 to be higher than 300 mg/kg. Moreover, 36b significantly reduced glycemia in an insulin tolerance test in mice, suggesting that its mechanism of action is through the PTP1B inhibition.
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Affiliation(s)
- Enrique Aguilar-Ramírez
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Valeria Reyes-Pérez
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Carlos A Fajardo-Hernández
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Carlos D Quezada-Suaste
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mario Carreón-Escalante
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Verenice Merlin-Lucas
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Beatriz Quiroz-García
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Vinicio Granados-Soto
- Pharmacobiology Department, Centro de Investigación y de Estudios Avanzados, Sede Sur, Mexico City 14330, Mexico
| | - José Rivera-Chávez
- Department of Natural Products, Institute of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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25
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Coronell-Tovar A, Cortés-Benítez F, González-Andrade M. The importance of including the C-terminal domain of PTP1B 1-400 to identify potential antidiabetic inhibitors. J Enzyme Inhib Med Chem 2023; 38:2170369. [PMID: 36997321 PMCID: PMC10064822 DOI: 10.1080/14756366.2023.2170369] [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: 04/01/2023] Open
Abstract
In the present work, we studied the inhibitory and kinetic implications of classical PTP1B inhibitors (chlorogenic acid, ursolic acid, suramin) using three enzyme constructs (hPTP1B1-285, hPTP1B1-321, and hPTP1B1-400). The results indicate that the unstructured region of PTP1B (300-400 amino acids) is very important both to obtain optimal inhibitory results and propose classical inhibition mechanisms (competitive or non-competitive) through kinetic studies. The IC50 calculated for ursolic acid and suramin using hPTP1B1-400 are around four and three times lower to the short form of the enzyme, the complete form of PTP1B, the one found in the cytosol (in vivo). On the other hand, we highlight the studies of enzymatic kinetics using the hPTP1B1-400 to know the type of enzymatic inhibition and to be able to direct docking studies, where the unstructured region of the enzyme can be one more option for binding compounds with inhibitory activity.
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Affiliation(s)
- Andrea Coronell-Tovar
- Departamento de Bioquímica, Facultad de Medicina, Laboratorio de Biosensores y Modelaje molecular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Francisco Cortés-Benítez
- Departamento de Sistemas Biológicos, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Xochimilco (UAM-X), Ciudad de México, México
| | - Martin González-Andrade
- Departamento de Bioquímica, Facultad de Medicina, Laboratorio de Biosensores y Modelaje molecular, Universidad Nacional Autónoma de México, Ciudad de México, México
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26
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Hu L, Li H, Qin J, Yang D, Liu J, Luo X, Ma J, Luo C, Ye F, Zhou Y, Li J, Wang M. Discovery of PVD-06 as a Subtype-Selective and Efficient PTPN2 Degrader. J Med Chem 2023; 66:15269-15287. [PMID: 37966047 DOI: 10.1021/acs.jmedchem.3c01348] [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: 11/16/2023]
Abstract
Protein tyrosine phosphatase nonreceptor Type 2 (PTPN2) is an attractive target for cancer immunotherapy. PTPN2 and another subtype of PTP1B are highly similar in structure, but their biological functions are distinct. Therefore, subtype-selective targeting of PTPN2 remains a challenge for researchers. Herein, the development of small molecular PTPN2 degraders based on a thiadiazolidinone dioxide-naphthalene scaffold and a VHL E3 ligase ligand is described, and the PTPN2/PTP1B subtype-selective degradation is achieved for the first time. The linker structure modifications led to the discovery of the subtype-selective PTPN2 degrader PVD-06 (PTPN2/PTP1B selective index > 60-fold), which also exhibits excellent proteome-wide degradation selectivity. PVD-06 induces PTPN2 degradation in a ubiquitination- and proteasome-dependent manner. It efficiently promotes T cell activation and amplifies IFN-γ-mediated B16F10 cell growth inhibition. This study provides a convenient chemical knockdown tool for PTPN2-related research and a paradigm for subtype-selective PTP degradation through nonspecific substrate-mimicking ligands, demonstrating the therapeutic potential of PTPN2 subtype-selective degradation.
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Affiliation(s)
- Linghao Hu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Huiyun Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, Guizhou China
| | - Junlin Qin
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Dan Yang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmaceutical Sciences, Southern Medical University, No.1023, South Shatai Road, Baiyun District, Guangzhou 510515, Guangdong, China
| | - Jieming Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Xiaomin Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | | | - Cheng Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yubo Zhou
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Jia Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, Guizhou China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmaceutical Sciences, Southern Medical University, No.1023, South Shatai Road, Baiyun District, Guangzhou 510515, Guangdong, China
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27
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Woods VA, Abzalimov RR, Keedy DA. Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548582. [PMID: 37503000 PMCID: PMC10369962 DOI: 10.1101/2023.07.12.548582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for obesity, diabetes, and certain types of cancer. In particular, allosteric inhibitors hold potential for therapeutic use, but an incomplete understanding of conformational dynamics and allostery in this protein has hindered their development. Here, we interrogate solution dynamics and allosteric responses in PTP1B using high-resolution hydrogen-deuterium exchange mass spectrometry (HDX-MS), an emerging and powerful biophysical technique. Using HDX-MS, we obtain a detailed map of the solution dynamics of apo PTP1B, revealing several flexible loops interspersed among more constrained and rigid regions within the protein structure, as well as local regions that exchange faster than expected from their secondary structure and buriedness. We demonstrate that our HDX rate data obtained in solution adds value to predictions of dynamics derived from a pseudo-ensemble constructed from ~200 crystal structures of PTP1B. Furthermore, we report HDX-MS maps for PTP1B with active-site vs. allosteric small-molecule inhibitors. These maps reveal distinct, dramatic, and widespread effects on protein dynamics relative to the apo form, including changes to dynamics in locations distal (>35 Å) from the respective ligand binding sites. These results help shed light on the allosteric nature of PTP1B and the surprisingly far-reaching consequences of inhibitor binding in this important protein. Overall, our work showcases the potential of HDX-MS for elucidating protein conformational dynamics and allosteric effects of small-molecule ligands, and highlights the potential of integrating HDX-MS alongside other complementary methods to guide the development of new therapeutics.
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Affiliation(s)
- Virgil A. Woods
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Rinat R. Abzalimov
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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28
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Schlicher L, Green LG, Romagnani A, Renner F. Small molecule inhibitors for cancer immunotherapy and associated biomarkers - the current status. Front Immunol 2023; 14:1297175. [PMID: 38022587 PMCID: PMC10644399 DOI: 10.3389/fimmu.2023.1297175] [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] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Following the success of cancer immunotherapy using large molecules against immune checkpoint inhibitors, the concept of using small molecules to interfere with intracellular negative regulators of anti-tumor immune responses has emerged in recent years. The main targets for small molecule drugs currently include enzymes of negative feedback loops in signaling pathways of immune cells and proteins that promote immunosuppressive signals within the tumor microenvironment. In the adaptive immune system, negative regulators of T cell receptor signaling (MAP4K1, DGKα/ζ, CBL-B, PTPN2, PTPN22, SHP1), co-receptor signaling (CBL-B) and cytokine signaling (PTPN2) have been preclinically validated as promising targets and initial clinical trials with small molecule inhibitors are underway. To enhance innate anti-tumor immune responses, inhibitory immunomodulation of cGAS/STING has been in the focus, and inhibitors of ENPP1 and TREX1 have reached the clinic. In addition, immunosuppressive signals via adenosine can be counteracted by CD39 and CD73 inhibition, while suppression via intratumoral immunosuppressive prostaglandin E can be targeted by EP2/EP4 antagonists. Here, we present the status of the most promising small molecule drug candidates for cancer immunotherapy, all residing relatively early in development, and the potential of relevant biomarkers.
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Affiliation(s)
- Lisa Schlicher
- Cancer Cell Targeted Therapy, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Luke G. Green
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Andrea Romagnani
- Cancer Cell Targeted Therapy, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Florian Renner
- Cancer Cell Targeted Therapy, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
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29
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Friedman AJ, Padgette HM, Kramer L, Liechty ET, Donovan GW, Fox JM, Shirts MR. Biophysical Rationale for the Selective Inhibition of PTP1B over TCPTP by Nonpolar Terpenoids. J Phys Chem B 2023; 127:8305-8316. [PMID: 37729547 PMCID: PMC10694825 DOI: 10.1021/acs.jpcb.3c03791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are emerging drug targets for many diseases, including cancer, autoimmunity, and neurological disorders. A high degree of structural similarity between their catalytic domains, however, has hindered the development of selective pharmacological agents. Our previous research uncovered two unfunctionalized terpenoid inhibitors that selectively inhibit PTP1B over T-cell PTP (TCPTP), two PTPs with high sequence conservation. Here, we use molecular modeling, with supporting experimental validation, to study the molecular basis of this unusual selectivity. Molecular dynamics (MD) simulations suggest that PTP1B and TCPTP share a h-bond network that connects the active site to a distal allosteric pocket; this network stabilizes the closed conformation of the catalytically essential WPD loop, which it links to the L-11 loop and neighboring α3 and α7 helices on the other side of the catalytic domain. Terpenoid binding to either of two proximal C-terminal sites─an α site and a β site─can disrupt the allosteric network; however, binding to the α site forms a stable complex only in PTP1B. In TCPTP, two charged residues disfavor binding at the α site in favor of binding at the β site, which is conserved between the two proteins. Our findings thus indicate that minor amino acid differences at the poorly conserved α site enable selective binding, a property that might be enhanced with chemical elaboration, and illustrate more broadly how minor differences in the conservation of neighboring─yet functionally similar─allosteric sites can affect the selectivity of inhibitory scaffolds (e.g., fragments).
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Affiliation(s)
- Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Hannah M Padgette
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Levi Kramer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Evan T Liechty
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Gregory W Donovan
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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30
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Bourebaba L, Serwotka-Suszczak A, Bourebaba N, Zyzak M, Marycz K. The PTP1B Inhibitor Trodusquemine (MSI-1436) Improves Glucose Uptake in Equine Metabolic Syndrome Affected Liver through Anti-Inflammatory and Antifibrotic Activity. Int J Inflam 2023; 2023:3803056. [PMID: 37808009 PMCID: PMC10560121 DOI: 10.1155/2023/3803056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/12/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Background Hyperactivation of protein tyrosine phosphatase (PTP1B) has been associated with several metabolic malfunctions ranging from insulin resistance, metaflammation, lipotoxicity, and hyperglycaemia. Liver metabolism failure has been proposed as a core element in underlying endocrine disorders through persistent inflammation and highly fibrotic phenotype. Methods In this study, the outcomes of PTP1B inhibition using trodusquemine (MSI-1436) on key equine metabolic syndrome (EMS)-related alterations including inflammation, fibrosis, and glucose uptake have been analyzed in liver explants collected from EMS-affected horses using various analytical techniques, namely, flow cytometry, RT-qPCR, and Western blot. Results PTP1B inhibition using trodusquemine resulted in decreased proinflammatory cytokines (IL-1β, TNF-α, and IL-6) release from liver and PBMC affected by EMS and regulated expression of major proinflammatory microRNAs such as miR-802 and miR-211. Moreover, MSI-1436 enhanced the anti-inflammatory profile of livers by elevating the expression of IL-10 and IL-4 and activating CD4+CD25+Foxp3+ regulatory T cells in treated PBMC. Similarly, the inhibitor attenuated fibrogenic pathways in the liver by downregulating TGF-β/NOX1/4 axis and associated MMP-2/9 overactivation. Interestingly, PTP1B inhibition ameliorated the expression of TIMP-1 and Smad7, both important antifibrotic mediators. Furthermore, application of MSI-1436 was found to augment the abundance of glycosylated Glut-2, which subsequently expanded the glucose absorption in the EMS liver, probably due to an enhanced Glut-2 stability and half-life onto the plasma cell membranes. Conclusion Taken together, the presented data suggest that the PTP1B inhibition strategy and the use of its specific inhibitor MSI-1436 represents a promising option for the improvement of liver tissue integrity and homeostasis in the course of EMS and adds more insights for ongoing clinical trials for human MetS management.
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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, Norwida 27B, Wrocław 50-375, Poland
| | - Anna Serwotka-Suszczak
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, Wrocław 50-375, Poland
| | - Nabila Bourebaba
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, Wrocław 50-375, Poland
| | - Magdalena Zyzak
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, Wrocław 50-375, Poland
| | - Krzysztof Marycz
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, Wrocław 50-375, Poland
- Department of Veterinary Medicine and Epidemiology, Veterinary Institute for Regenerative Cures, School of Veterinary Medicine, University of California, Davis, CA 95516, USA
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31
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023; 688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [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] [Indexed: 09/27/2023]
Abstract
Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, United States.
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32
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Qian Z, Song D, Ipsaro JJ, Bautista C, Joshua-Tor L, Yeh JTH, Tonks NK. Manipulating PTPRD function with ectodomain antibodies. Genes Dev 2023; 37:743-759. [PMID: 37669874 PMCID: PMC10546974 DOI: 10.1101/gad.350713.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/28/2023] [Indexed: 09/07/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are critical regulators of signal transduction but have yet to be exploited fully for drug development. Receptor protein tyrosine phosphatase δ (RPTPδ/PTPRD) has been shown to elicit tumor-promoting functions, including elevating SRC activity and promoting metastasis in certain cell contexts. Dimerization has been implicated in the inhibition of receptor protein tyrosine phosphatases (RPTPs). We have generated antibodies targeting PTPRD ectodomains with the goal of manipulating their dimerization status ectopically, thereby regulating intracellular signaling. We have validated antibody binding to endogenous PTPRD in a metastatic breast cancer cell line, CAL51, and demonstrated that a monoclonal antibody, RD-43, inhibited phosphatase activity and induced the degradation of PTPRD. Similar effects were observed following chemically induced dimerization of its phosphatase domain. Mechanistically, RD-43 triggered the formation of PTPRD dimers in which the phosphatase activity was impaired. Subsequently, the mAb-PTPRD dimer complex was degraded through lysosomal and proteasomal pathways, independently of secretase cleavage. Consequently, treatment with RD-43 inhibited SRC signaling and suppressed PTPRD-dependent cell invasion. Together, these findings demonstrate that manipulating RPTP function via antibodies to the extracellular segments has therapeutic potential.
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Affiliation(s)
- Zhe Qian
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Graduate Program of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11760, USA
| | - Dongyan Song
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Johannes T-H Yeh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
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33
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Liang S, Tran E, Du X, Dong J, Sudholz H, Chen H, Qu Z, Huntington ND, Babon JJ, Kershaw NJ, Zhang ZY, Baell JB, Wiede F, Tiganis T. A small molecule inhibitor of PTP1B and PTPN2 enhances T cell anti-tumor immunity. Nat Commun 2023; 14:4524. [PMID: 37500611 PMCID: PMC10374545 DOI: 10.1038/s41467-023-40170-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023] Open
Abstract
The inhibition of protein tyrosine phosphatases 1B (PTP1B) and N2 (PTPN2) has emerged as an exciting approach for bolstering T cell anti-tumor immunity. ABBV-CLS-484 is a PTP1B/PTPN2 inhibitor in clinical trials for solid tumors. Here we have explored the therapeutic potential of a related small-molecule-inhibitor, Compound-182. We demonstrate that Compound-182 is a highly potent and selective active site competitive inhibitor of PTP1B and PTPN2 that enhances T cell recruitment and activation and represses the growth of tumors in mice, without promoting overt immune-related toxicities. The enhanced anti-tumor immunity in immunogenic tumors can be ascribed to the inhibition of PTP1B/PTPN2 in T cells, whereas in cold tumors, Compound-182 elicited direct effects on both tumor cells and T cells. Importantly, treatment with Compound-182 rendered otherwise resistant tumors sensitive to α-PD-1 therapy. Our findings establish the potential for small molecule inhibitors of PTP1B and PTPN2 to enhance anti-tumor immunity and combat cancer.
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Affiliation(s)
- Shuwei Liang
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Eric Tran
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Xin Du
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Harrison Sudholz
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Hao Chen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Nicholas D Huntington
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jeffrey J Babon
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
- Lyterian Therapeutics, South San Francisco, San Francisco, CA, 94080, USA
| | - Florian Wiede
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
| | - Tony Tiganis
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
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Sendo S, Kiosses WB, Yang S, Wu DJ, Lee DWK, Liu L, Aschner Y, Vela AJ, Downey GP, Santelli E, Bottini N. Clustering of phosphatase RPTPα promotes Src signaling and the arthritogenic action of synovial fibroblasts. Sci Signal 2023; 16:eabn8668. [PMID: 37402225 PMCID: PMC10544828 DOI: 10.1126/scisignal.abn8668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 06/15/2023] [Indexed: 07/06/2023]
Abstract
Receptor-type protein phosphatase α (RPTPα) promotes fibroblast-dependent arthritis and fibrosis, in part, by enhancing the activation of the kinase SRC. Synovial fibroblasts lining joint tissue mediate inflammation and tissue damage, and their infiltration into adjacent tissues promotes disease progression. RPTPα includes an ectodomain and two intracellular catalytic domains (D1 and D2) and, in cancer cells, undergoes inhibitory homodimerization, which is dependent on a D1 wedge motif. Through single-molecule localization and labeled molecule interaction microscopy of migrating synovial fibroblasts, we investigated the role of RPTPα dimerization in the activation of SRC, the migration of synovial fibroblasts, and joint damage in a mouse model of arthritis. RPTPα clustered with other RPTPα and with SRC molecules in the context of actin-rich structures. A known dimerization-impairing mutation in the wedge motif (P210L/P211L) and the deletion of the D2 domain reduced RPTPα-RPTPα clustering; however, it also unexpectedly reduced RPTPα-SRC association. The same mutations also reduced recruitment of RPTPα to actin-rich structures and inhibited SRC activation and cellular migration. An antibody against the RPTPα ectodomain that prevented the clustering of RPTPα also inhibited RPTPα-SRC association and SRC activation and attenuated fibroblast migration and joint damage in arthritic mice. A catalytically inactivating RPTPα-C469S mutation protected mice from arthritis and reduced SRC activation in synovial fibroblasts. We conclude that RPTPα clustering retains it to actin-rich structures to promote SRC-mediated fibroblast migration and can be modulated through the extracellular domain.
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Affiliation(s)
- Sho Sendo
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - William B. Kiosses
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Shen Yang
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Dennis J. Wu
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Daniel W. K. Lee
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Lin Liu
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Yael Aschner
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado
| | - Allison J. Vela
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Gregory P. Downey
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
- Department of Pediatrics, National Jewish Health, Denver, Colorado
| | - Eugenio Santelli
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Nunzio Bottini
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, Kao Autoimmunity Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
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Bartolomé RA, Casal JI. Proteomic profiling and network biology of colorectal cancer liver metastasis. Expert Rev Proteomics 2023; 20:357-370. [PMID: 37874121 DOI: 10.1080/14789450.2023.2275681] [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: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
INTRODUCTION Tissue-based proteomic studies of colorectal cancer (CRC) metastasis have delivered fragmented results, with very few therapeutic targets and prognostic biomarkers moving beyond the discovery phase. This situation is likely due to the difficulties in obtaining and analyzing large numbers of patient-derived metastatic samples, the own heterogeneity of CRC, and technical limitations in proteomics discovery. As an alternative, metastatic CRC cell lines provide a flexible framework to investigate the underlying mechanisms and network biology of metastasis for target discovery. AREAS COVERED In this perspective, we comment on different in-depth proteomic studies of metastatic versus non-metastatic CRC cell lines. Identified metastasis-related proteins are introduced and discussed according to the spatial location in different cellular fractions, with special emphasis on membrane/adhesion proteins, secreted proteins, and nuclear factors, including miRNAs associated with liver metastasis. Moreover, we analyze the biological significance and potential therapeutic applications of the identified liver metastasis-related proteins. EXPERT OPINION The combination of protein discovery and functional analysis is the only way to accelerate the progress to clinical translation of the proteomic-derived findings in a relatively fast pace. Patient-derived organoids represent a promising alternative to patient tissues and cell lines, but further optimizations are still required for achieving solid and reproducible results.
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Affiliation(s)
- Rubén A Bartolomé
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas Margarita Salas, Madrid, Spain
| | - J Ignacio Casal
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas Margarita Salas, Madrid, Spain
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Liang S, Tran E, Du X, Dong J, Sudholz H, Chen H, Qu Z, Huntington N, Babon J, Kershaw N, Zhang ZY, Baell J, Wiede F, Tiganis T. A small molecule inhibitor of PTP1B and PTPN2 enhances T cell anti-tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545220. [PMID: 37397992 PMCID: PMC10312756 DOI: 10.1101/2023.06.16.545220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The inhibition of protein tyrosine phosphatases (PTPs), such as PTP1B and PTPN2 that function as intracellular checkpoints, has emerged as an exciting new approach for bolstering T cell anti-tumor immunity to combat cancer. ABBV-CLS-484 is a dual PTP1B and PTPN2 inhibitor currently in clinical trials for solid tumors. Here we have explored the therapeutic potential of targeting PTP1B and PTPN2 with a related small molecule inhibitor, Compound 182. We demonstrate that Compound 182 is a highly potent and selective active site competitive inhibitor of PTP1B and PTPN2 that enhances antigen-induced T cell activation and expansion ex vivo and represses the growth of syngeneic tumors in C57BL/6 mice without promoting overt immune-related toxicities. Compound 182 repressed the growth of immunogenic MC38 colorectal and AT3-OVA mammary tumors as well as immunologically cold AT3 mammary tumors that are largely devoid of T cells. Treatment with Compound 182 increased both the infiltration and activation of T cells, as well as the recruitment of NK cells and B cells that promote anti-tumor immunity. The enhanced anti-tumor immunity in immunogenic AT3-OVA tumors could be ascribed largely to the inhibition of PTP1B/PTPN2 in T cells, whereas in cold AT3 tumors, Compound 182 elicited both direct effects on tumor cells and T cells to facilitate T cell recruitment and thereon activation. Importantly, treatment with Compound 182 rendered otherwise resistant AT3 tumors sensitive to anti-PD1 therapy. Our findings establish the potential for small molecule active site inhibitors of PTP1B and PTPN2 to enhance anti-tumor immunity and combat cancer.
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37
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Maccari R, Ottanà R. Can Allostery Be a Key Strategy for Targeting PTP1B in Drug Discovery? A Lesson from Trodusquemine. Int J Mol Sci 2023; 24:ijms24119621. [PMID: 37298571 DOI: 10.3390/ijms24119621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an enzyme crucially implicated in aberrations of various signaling pathways that underlie the development of different human pathologies, such as obesity, diabetes, cancer, and neurodegenerative disorders. Its inhibition can prevent these pathogenetic events, thus providing a useful tool for the discovery of novel therapeutic agents. The search for allosteric PTP1B inhibitors can represent a successful strategy to identify drug-like candidates by offering the opportunity to overcome some issues related to catalytic site-directed inhibitors, which have so far hampered the development of drugs targeting this enzyme. In this context, trodusquemine (MSI-1436), a natural aminosterol that acts as a non-competitive PTP1B inhibitor, appears to be a milestone. Initially discovered as a broad-spectrum antimicrobial agent, trodusquemine exhibited a variety of unexpected properties, ranging from antidiabetic and anti-obesity activities to effects useful to counteract cancer and neurodegeneration, which prompted its evaluation in several preclinical and clinical studies. In this review article, we provide an overview of the main findings regarding the activities and therapeutic potential of trodusquemine and their correlation with PTP1B inhibition. We also included some aminosterol analogues and related structure-activity relationships that could be useful for further studies aimed at the discovery of new allosteric PTP1B inhibitors.
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Affiliation(s)
- Rosanna Maccari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Rosaria Ottanà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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38
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Yang JB, Yang CS, Li J, Su GZ, Tian JY, Wang Y, Liu Y, Wei F, Li Y, Ye F, Ma SC. Dianthrone derivatives from Polygonum multiflorum Thunb: Anti-diabetic activity, structure-activity relationships (SARs), and mode of action. Bioorg Chem 2023; 135:106491. [PMID: 37011521 DOI: 10.1016/j.bioorg.2023.106491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
PTP1B plays an important role as a key negative regulator of tyrosine phosphorylation associated with insulin receptor signaling in the therapy for diabetes and obesity. In this study, the anti-diabetic activity of dianthrone derivatives from Polygonum multiflorum Thunb., as well as the structure-activity relationships, mechanism, and molecular docking were explored. Among these analogs, trans-emodin dianthrone (compound 1) enhances insulin sensitivity by upregulating the insulin signaling pathway in HepG2 cells and displays considerable anti-diabetic activity in db/db mice. By using photoaffinity labeling and mass spectrometry-based proteomics, we discovered that trans-emodin dianthrone (compound 1) may bind to PTP1B allosteric pocket at helix α6/α7, which provides fresh insight into the identification of novel anti-diabetic agents.
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Affiliation(s)
- Jian-Bo Yang
- National Institutes for Food and Drug Control, Beijing 100050, China; Xinjiang Uygur Autonomous Region Institute for Drug Control, Urumqi 830054, China
| | - Cheng-Shuo Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jiang Li
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China; Diabetes Research Center of Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guo-Zhu Su
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jin-Ying Tian
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China; Diabetes Research Center of Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ying Wang
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yue Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Feng Wei
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yong Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Fei Ye
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China; Diabetes Research Center of Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Shuang-Cheng Ma
- National Institutes for Food and Drug Control, Beijing 100050, China.
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Zheng LE, Barethiya S, Nordquist E, Chen J. Machine Learning Generation of Dynamic Protein Conformational Ensembles. Molecules 2023; 28:4047. [PMID: 37241789 PMCID: PMC10220786 DOI: 10.3390/molecules28104047] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Machine learning has achieved remarkable success across a broad range of scientific and engineering disciplines, particularly its use for predicting native protein structures from sequence information alone. However, biomolecules are inherently dynamic, and there is a pressing need for accurate predictions of dynamic structural ensembles across multiple functional levels. These problems range from the relatively well-defined task of predicting conformational dynamics around the native state of a protein, which traditional molecular dynamics (MD) simulations are particularly adept at handling, to generating large-scale conformational transitions connecting distinct functional states of structured proteins or numerous marginally stable states within the dynamic ensembles of intrinsically disordered proteins. Machine learning has been increasingly applied to learn low-dimensional representations of protein conformational spaces, which can then be used to drive additional MD sampling or directly generate novel conformations. These methods promise to greatly reduce the computational cost of generating dynamic protein ensembles, compared to traditional MD simulations. In this review, we examine recent progress in machine learning approaches towards generative modeling of dynamic protein ensembles and emphasize the crucial importance of integrating advances in machine learning, structural data, and physical principles to achieve these ambitious goals.
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Affiliation(s)
- Li-E Zheng
- Department of Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China;
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
| | - Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
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40
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Marycz K, Bourebaba N, Serwotka-Suszczak A, Mularczyk M, Galuppo L, Bourebaba L. In Vitro Generated Equine Hepatic-Like Progenitor Cells as a Novel Potent Cell Pool for Equine Metabolic Syndrome (EMS) Treatment. Stem Cell Rev Rep 2023; 19:1124-1134. [PMID: 36658383 PMCID: PMC10185601 DOI: 10.1007/s12015-023-10507-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
Equine metabolic syndrome (EMS) is recognized as one of the leading cause of health threatening in veterinary medicine worldwide. Recently, PTP1B inhibition has been proposed as an interesting strategy for liver insulin resistance reversion in both equines and humans, however as being a multifactorial disease, proper management of EMS horses further necessities additional interventional approaches aiming at repairing and restoring liver functions. In this study, we hypothesized that in vitro induction of Eq_ASCs hepatogenic differentiation will generate a specialized liver progenitor-like cell population exhibiting similar phenotypic characteristics and regenerative potential as native hepatic progenitor cells. Our obtained data demonstrated that Eq_ASCs-derived liver progenitor cells (Eq_HPCs) displayed typical flattened polygonal morphology with packed fragmented mitochondrial net, lowered mesenchymal CD105 and CD90 surface markers expression, and significant high expression levels of specific hepatic lineage genes including PECAM-1, ALB, AFP and HNF4A. therewith, generated Eq_HPCs exhibited potentiated stemness and pluripotency markers expression (NANOG, SOX-2 and OCT-4). Hence, in vitro generation of hepatic progenitor-like cells retaining high differentiation capacity represents a promising new approach for the establishment of cell-based targeted therapies for the restoration of proper liver functions in EMS affected horses.
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Affiliation(s)
- Krzysztof Marycz
- International Institute of Translational Medicine, Jesionowa 11, Malin, 55-114, Wisznia Mała, Poland.
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, 95516, USA.
| | - Nabila Bourebaba
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, 50-375, Wrocław, Poland
| | - Anna Serwotka-Suszczak
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, 50-375, Wrocław, Poland
| | - Malwina Mularczyk
- International Institute of Translational Medicine, Jesionowa 11, Malin, 55-114, Wisznia Mała, Poland
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, 50-375, Wrocław, Poland
| | - Larry Galuppo
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, 95516, USA
| | - Lynda Bourebaba
- Department of Experimental Biology, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Norwida 27B, 50-375, Wrocław, Poland.
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41
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Bennett AM. Teaching an old dog new tricks: A new tool for protein tyrosine phosphatase substrate discovery. J Biol Chem 2023; 299:104731. [PMID: 37080392 PMCID: PMC10193000 DOI: 10.1016/j.jbc.2023.104731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2023] [Indexed: 04/22/2023] Open
Abstract
The identification of substrates for protein tyrosine phosphatases (PTPs) is critical for a complete understanding of how these enzymes function. In a recent study in the JBC, Bonham et al. developed a modified method combining substrate-trapping mutations with proximity-labeling MS to identify the protein substrates and interactors of PTP1B. This method revealed interaction networks in breast cancer cell models and discovered novel targets of PTP1B that regulate HER2 signaling pathways. This strategy represents a versatile new tool for identifying the functional interactions between PTPs and their substrates.
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Affiliation(s)
- Anton M Bennett
- Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut, USA; Yale University School of Medicine, Yale Center for Molecular and Systems Metabolism, New Haven, Connecticut, USA.
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42
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Friedman AJ, Padgette HM, Kramer L, Liechty ET, Donovan GW, Fox JM, Shirts MR. A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537234. [PMID: 37131728 PMCID: PMC10153121 DOI: 10.1101/2023.04.17.537234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are emerging drug targets for many diseases, including type 2 diabetes, obesity, and cancer. However, a high degree of structural similarity between the catalytic domains of these enzymes has made the development of selective pharmacological inhibitors an enormous challenge. Our previous research uncovered two unfunctionalized terpenoid inhibitors that selectively inhibit PTP1B over TCPTP, two PTPs with high sequence conservation. Here, we use molecular modeling with experimental validation to study the molecular basis of this unusual selectivity. Molecular dynamics (MD) simulations indicate that PTP1B and TCPTP contain a conserved h-bond network that connects the active site to a distal allosteric pocket; this network stabilizes the closed conformation of the catalytically influential WPD loop, which it links to the L-11 loop and α 3 and α 7 helices-the C-terminal side of the catalytic domain. Terpenoid binding to either of two proximal allosteric sites-an α site and a β site-can disrupt the allosteric network. Interestingly, binding to the α site forms a stable complex with only PTP1B; in TCPTP, where two charged residues disfavor binding at the α site, the terpenoids bind to the β site, which is conserved between the two proteins. Our findings indicate that minor amino acid differences at the poorly conserved α site enable selective binding, a property that might be enhanced with chemical elaboration, and illustrate, more broadly, how minor differences in the conservation of neighboring-yet functionally similar-allosteric sites can have very different implications for inhibitor selectivity.
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Affiliation(s)
- Anika J Friedman
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Hannah M Padgette
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Levi Kramer
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Evan T Liechty
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Gregory W Donovan
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Jerome M Fox
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Michael R Shirts
- University of Colorado Boulder Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
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43
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Tonks NK. Protein Tyrosine Phosphatases: Mighty oaks from little acorns grow. IUBMB Life 2023; 75:337-352. [PMID: 36971473 PMCID: PMC10254075 DOI: 10.1002/iub.2716] [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: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/29/2023]
Abstract
In October 2020, we were finally able to gather for a celebration of Eddy Fischer's 100th birthday. As with many other events, COVID had disrupted and restricted preparations for the gathering, which ultimately was held via ZOOM. Nevertheless, it was a wonderful opportunity to share a day with Eddy, an exceptional scientist and true renaissance man, and to appreciate his stellar contributions to science. Eddy Fischer, together with Ed Krebs, was responsible for the discovery of reversible protein phosphorylation, which launched the entire field of signal transduction. The importance of this seminal work is now being felt throughout the biotechnology industry with the development of drugs that target protein kinases, which have transformed the treatment of a wide array of cancers. I was privileged to have worked with Eddy both as a postdoc and a junior faculty member, during which time we laid the foundations for our current understanding of the protein tyrosine phosphatase (PTP) family of enzymes and their importance as critical regulators of signal transduction. This tribute to Eddy is based upon the talk I presented at the event, giving a personal perspective on Eddy's influence on my career, our early research efforts together in this area, and how the field has developed since then.
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Affiliation(s)
- Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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44
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Saurabh S, Nadendla K, Purohit SS, Sivakumar PM, Cetinel S. Fuzzy Drug Targets: Disordered Proteins in the Drug-Discovery Realm. ACS OMEGA 2023; 8:9729-9747. [PMID: 36969402 PMCID: PMC10034788 DOI: 10.1021/acsomega.2c07708] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) form a large part of the eukaryotic proteome. Contrary to the structure-function paradigm, the disordered proteins perform a myriad of functions in vivo. Consequently, they are involved in various disease pathways and are plausible drug targets. Unlike folded proteins, that have a defined structure and well carved out drug-binding pockets that can guide lead molecule selection, the disordered proteins require alternative drug-development methodologies that are based on an acceptable picture of their conformational ensemble. In this review, we discuss various experimental and computational techniques that contribute toward understanding IDP "structure" and describe representative pursuances toward IDP-targeting drug development. We also discuss ideas on developing rational drug design protocols targeting IDPs.
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Affiliation(s)
- Suman Saurabh
- Molecular
Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Karthik Nadendla
- Center
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Lensfield
Road, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Shubh Sanket Purohit
- Department
of Clinical Haematology, Sahyadri Superspeciality
Hospital, Pune, Maharashtra 411038, India
| | - Ponnurengam Malliappan Sivakumar
- Institute
of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
- School
of Medicine and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
| | - Sibel Cetinel
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
- Faculty of
Engineering and Natural Sciences, Molecular Biology, Genetics and
Bioengineering Program, Sabanci University, Istanbul 34956, Turkey
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45
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Skaist Mehlman T, Biel JT, Azeem SM, Nelson ER, Hossain S, Dunnett L, Paterson NG, Douangamath A, Talon R, Axford D, Orins H, von Delft F, Keedy DA. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B. eLife 2023; 12:84632. [PMID: 36881464 PMCID: PMC9991056 DOI: 10.7554/elife.84632] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/12/2023] [Indexed: 03/08/2023] Open
Abstract
Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. We show that at RT, fewer ligands bind, and often more weakly - but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function.
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Affiliation(s)
- Tamar Skaist Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- PhD Program in Biochemistry, CUNY Graduate CenterNew YorkUnited States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Syeda Maryam Azeem
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | | | - Sakib Hossain
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Louise Dunnett
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | | | - Alice Douangamath
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | | | | | - Helen Orins
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Frank von Delft
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Biochemistry, University of JohannesburgJohannesburgSouth Africa
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Department of Chemistry and Biochemistry, City College of New YorkNew YorkUnited States
- PhD Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate CenterNew YorkUnited States
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46
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Bonham C, Mandati V, Singh R, Pappin D, Tonks N. Coupling substrate-trapping with proximity-labeling to identify protein tyrosine phosphatase PTP1B signaling networks. J Biol Chem 2023; 299:104582. [PMID: 36871762 PMCID: PMC10148153 DOI: 10.1016/j.jbc.2023.104582] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 03/06/2023] Open
Abstract
The ability to define functional interactions between enzymes and their substrates is crucial for understanding biological control mechanisms; however, such methods face challenges in the transient nature and low stoichiometry of enzyme-substrate interactions. Now, we have developed an optimized strategy that couples substrate-trapping mutagenesis to proximity-labeling mass spectrometry for quantitative analysis of protein complexes involving the protein tyrosine phosphatase PTP1B. This methodology represents a significant shift from classical schemes; it is capable of being performed at near-endogenous expression levels and increasing stoichiometry of target enrichment without a requirement for stimulation of supraphysiological tyrosine phosphorylation levels or maintenance of substrate complexes during lysis and enrichment procedures. Advantages of this new approach are illustrated through application to PTP1B interaction networks in models of HER2-positive and Herceptin-resistant breast cancer. We have demonstrated that inhibitors of PTP1B significantly reduced proliferation and viability in cell-based models of acquired and de novo Herceptin resistance in HER2-positive breast cancer. Using differential analysis, comparing substrate-trapping to wild-type PTP1B, we have identified multiple unreported protein targets of PTP1B with established links to HER2-induced signaling and provided internal validation of method specificity through overlap with previously identified substrate candidates. Overall, this versatile approach can be readily integrated with evolving proximity-labeling platforms (TurboID, BioID2, etc.), and is broadly applicable across all PTP family members for the identification of conditional substrate specificities and signaling nodes in models of human disease.
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Affiliation(s)
- ChristopherA Bonham
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Vinay Mandati
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - RakeshK Singh
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - DarrylJ Pappin
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - NicholasK Tonks
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Derkach KV, Gureev MA, Babushkina AA, Mikhaylov VN, Zakharova IO, Bakhtyukov AA, Sorokoumov VN, Novikov AS, Krasavin M, Shpakov AO, Balova IA. Dual PTP1B/TC-PTP Inhibitors: Biological Evaluation of 3-(Hydroxymethyl)cinnoline-4( 1H)-Ones. Int J Mol Sci 2023; 24:ijms24054498. [PMID: 36901928 PMCID: PMC10002984 DOI: 10.3390/ijms24054498] [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: 02/02/2023] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Dual inhibitors of protein phosphotyrosine phosphatase 1B (PTP1B)/T-cell protein phosphotyrosine phosphatase (TC-PTP) based on the 3-(hydroxymethyl)-4-oxo-1,4-dihydrocinnoline scaffold have been identified. Their dual affinity to both enzymes has been thoroughly corroborated by in silico modeling experiments. The compounds have been profiled in vivo for their effects on body weight and food intake in obese rats. Likewise, the effects of the compounds on glucose tolerance, insulin resistance, as well as insulin and leptin levels, have been evaluated. In addition, the effects on PTP1B, TC-PTP, and Src homology region 2 domain-containing phosphatase-1 (SHP1), as well as the insulin and leptin receptors gene expressions, have been assessed. In obese male Wistar rats, a five-day administration of all studied compounds led to a decrease in body weight and food intake, improved glucose tolerance, attenuated hyperinsulinemia, hyperleptinemia and insulin resistance, and also compensatory increased expression of the PTP1B and TC-PTP genes in the liver. The highest activity was demonstrated by 6-Chloro-3-(hydroxymethyl)cinnolin-4(1H)-one (compound 3) and 6-Bromo-3-(hydroxymethyl)cinnolin-4(1H)-one (compound 4) with mixed PTP1B/TC-PTP inhibitory activity. Taken together, these data shed light on the pharmacological implications of PTP1B/TC-PTP dual inhibition, and on the promise of using mixed PTP1B/TC-PTP inhibitors to correct metabolic disorders.
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Affiliation(s)
- Kira V. Derkach
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez av. 44, 194223 St. Petersburg, Russia
| | - Maxim A. Gureev
- Center of Bio- and Chemoinformatics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Anastasia A. Babushkina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Vladimir N. Mikhaylov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Irina O. Zakharova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez av. 44, 194223 St. Petersburg, Russia
| | - Andrey A. Bakhtyukov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez av. 44, 194223 St. Petersburg, Russia
| | - Viktor N. Sorokoumov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Alexander S. Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Mikhail Krasavin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
- Institute for Medicine and Life Sciences, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
| | - Alexander O. Shpakov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez av. 44, 194223 St. Petersburg, Russia
| | - Irina A. Balova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-428-6733
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48
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Artificial Intelligence-Based Computational Screening and Functional Assays Identify Candidate Small Molecule Antagonists of PTPmu-Dependent Adhesion. Int J Mol Sci 2023; 24:ijms24054274. [PMID: 36901713 PMCID: PMC10001486 DOI: 10.3390/ijms24054274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/25/2023] Open
Abstract
PTPmu (PTPµ) is a member of the receptor protein tyrosine phosphatase IIb family that participates in cell-cell adhesion and signaling. PTPmu is proteolytically downregulated in glioblastoma (glioma), and the resulting extracellular and intracellular fragments are believed to stimulate cancer cell growth and/or migration. Therefore, drugs targeting these fragments may have therapeutic potential. Here, we used the AtomNet® platform, the first deep learning neural network for drug design and discovery, to screen a molecular library of several million compounds and identified 76 candidates predicted to interact with a groove between the MAM and Ig extracellular domains required for PTPmu-mediated cell adhesion. These candidates were screened in two cell-based assays: PTPmu-dependent aggregation of Sf9 cells and a tumor growth assay where glioma cells grow in three-dimensional spheres. Four compounds inhibited PTPmu-mediated aggregation of Sf9 cells, six compounds inhibited glioma sphere formation/growth, while two priority compounds were effective in both assays. The stronger of these two compounds inhibited PTPmu aggregation in Sf9 cells and inhibited glioma sphere formation down to 25 micromolar. Additionally, this compound was able to inhibit the aggregation of beads coated with an extracellular fragment of PTPmu, directly demonstrating an interaction. This compound presents an interesting starting point for the development of PTPmu-targeting agents for treating cancer including glioblastoma.
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49
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Targeting protein phosphatases in cancer immunotherapy and autoimmune disorders. Nat Rev Drug Discov 2023; 22:273-294. [PMID: 36693907 PMCID: PMC9872771 DOI: 10.1038/s41573-022-00618-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 01/25/2023]
Abstract
Protein phosphatases act as key regulators of multiple important cellular processes and are attractive therapeutic targets for various diseases. Although extensive effort has been dedicated to phosphatase-targeted drug discovery, early expeditions for competitive phosphatase inhibitors were plagued by druggability issues, leading to the stigmatization of phosphatases as difficult targets. Despite challenges, persistent efforts have led to the identification of several drug-like, non-competitive modulators of some of these enzymes - including SH2 domain-containing protein tyrosine phosphatase 2, protein tyrosine phosphatase 1B, vascular endothelial protein tyrosine phosphatase and protein phosphatase 1 - reigniting interest in therapeutic targeting of phosphatases. Here, we discuss recent progress in phosphatase drug discovery, with emphasis on the development of selective modulators that exhibit biological activity. The roles and regulation of protein phosphatases in immune cells and their potential as powerful targets for immuno-oncology and autoimmunity indications are assessed.
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50
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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