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Shi C, Chang L, Wang J, Dai J, Xu W, Tang J, Mei W, Zhang C, Wang Z, Liao Y, Zhang X, Jiang W, Zhang G, Zhao Z, Xu Y, Zhu L, Li H. Discovery of Novel Non-Nucleoside Inhibitors Interacting with Dizinc Ions of CD73. J Med Chem 2024. [PMID: 38809692 DOI: 10.1021/acs.jmedchem.4c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
High extracellular concentrations of adenosine triphosphate (ATP) in the tumor microenvironment generate adenosine by sequential dephosphorylation of CD39 and CD73, resulting in potent immunosuppression to inhibit T cell and natural killer (NK) cell function. CD73, as the determining enzyme for adenosine production, has been shown to correlate with poor clinical tumor prognosis. Conventional inhibitors as analogues of adenosine 5'-monophosphate (AMP) may have a risk of further metabolism to adenosine analogues. Here, we report a new series of malonic acid non-nucleoside inhibitors coordinating with zinc ions of CD73. Compound 12f was found to be a superior CD73 inhibitor (IC50 = 60 nM) by structural optimization, and its pharmacokinetic properties were investigated. In mouse tumor models, compound 12f showed excellent efficacy and reversal of immunosuppression in combination with chemotherapeutic agents or checkpoint inhibitors, suggesting that it deserves further development as a novel CD73 inhibitor.
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Affiliation(s)
- Cunjian Shi
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Longfeng Chang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jingqi Dai
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenyue Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiangyang Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenyi Mei
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zedong Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yichen Liao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xingsen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenzhe Jiang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guozhen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China
- Lingang Laboratory, Shanghai 200031, China
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Mihajlovic K, Bukvic MA, Dragic M, Scortichini M, Jacobson KA, Nedeljkovic N. Anti-inflammatory potency of novel ecto-5'-nucleotidase/CD73 inhibitors in astrocyte culture model of neuroinflammation. Eur J Pharmacol 2023; 956:175943. [PMID: 37541364 PMCID: PMC10527948 DOI: 10.1016/j.ejphar.2023.175943] [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: 05/16/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Three novel cytosine-derived α,β-methylene diphosphonates designated MRS4598, MRS4552, and MRS4602 were tested in the range of 1 × 10-9 to 1 × 10-3 M for their efficacy and potency in inhibiting membrane-bound ecto-5'-nucleotidase/CD73 activity in primary astrocytes in vitro. The compounds were also tested for their ability to attenuate the reactive astrocyte phenotype induced by proinflammatory cytokines. The main findings are as follows: A) The tested compounds induced concentration-dependent inhibition of CD73 activity, with maximal inhibition achieved at ∼1 × 10-3M; B) All compounds showed high inhibitory potency, as reflected by IC50 values in the submicromolar range; C) All compounds showed high binding capacity, as reflected by Ki values in the low nanomolar range; D) Among the tested compounds, MRS4598 showed the highest inhibitory efficacy and potency, as reflected by IC50 and Ki values of 0.11 μM and 18.2 nM; E) Neither compound affected astrocyte proliferation and cell metabolic activity at concentrations near to IC50; E) MRS4598 was able to inhibit CD73 activity in reactive astrocytes stimulated with TNF-α and to induce concentration-dependent inhibition of CD73 in reactive astrocytes stimulated with IL-1β, with an order of magnitude higher IC50 value; F) MRS4598 was the only compound tested that was able to induce shedding of the CD73 from astrocyte membranes and to enhance astrocyte migration in the scratch wound migration assay, albeit at concentration well above its IC50 value. Given the role of CD73 in neurodegenerative diseases, MRS4598, MRS4552, and MRS4602 are promising pharmacological tools for the treatment of neurodegeneration and neuroinflammation.
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Affiliation(s)
- Katarina Mihajlovic
- Laboratory for Neurobiology, Department of General Physiology and Biophysics, Faculty of Biology University of Belgrade, Serbia
| | - Marija Adzic Bukvic
- Laboratory for Neurobiology, Department of General Physiology and Biophysics, Faculty of Biology University of Belgrade, Serbia
| | - Milorad Dragic
- Laboratory for Neurobiology, Department of General Physiology and Biophysics, Faculty of Biology University of Belgrade, Serbia
| | - Mirko Scortichini
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nadezda Nedeljkovic
- Laboratory for Neurobiology, Department of General Physiology and Biophysics, Faculty of Biology University of Belgrade, Serbia.
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Viviani LG, Kokh DB, Wade RC, T-do Amaral A. Molecular Dynamics Simulations of the Human Ecto-5'-Nucleotidase (h-ecto-5'-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. J Chem Inf Model 2023; 63:4691-4707. [PMID: 37532679 DOI: 10.1021/acs.jcim.3c01068] [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: 08/04/2023]
Abstract
Human ecto-5'-nucleotidase (h-ecto-5'-NT, CD73) is a homodimeric Zn2+-binding metallophosphoesterase that hydrolyzes adenosine 5'-monophosphate (5'-AMP) to adenosine and phosphate. h-Ecto-5'-NT is a key enzyme in purinergic signaling pathways and has been recognized as a promising biological target for several diseases, including cancer and inflammatory, infectious, and autoimmune diseases. Despite its importance as a biological target, little is known about h-ecto-5'-NT dynamics, which poses a considerable challenge to the design of inhibitors of this target enzyme. Here, to explore h-ecto-5'-NT flexibility, all-atom unbiased molecular dynamics (MD) simulations were performed. Remarkable differences in the dynamics of the open (catalytically inactive) and closed (catalytically active) conformations of the apo-h-ecto-5'-NT were observed during the simulations, and the nucleotide analogue inhibitor AMPCP was shown to stabilize the protein structure in the closed conformation. Our results suggest that the large and complex domain motion that enables the h-ecto-5'-NT open/closed conformational switch is slow, and therefore, it could not be completely captured within the time scale of our simulations. Nonetheless, we were able to explore the faster dynamics of the h-ecto-5'-NT substrate binding site, which is mainly located at the C-terminal domain and well conserved among the protein's open and closed conformations. Using the TRAPP ("Transient Pockets in Proteins") approach, we identified transient subpockets close to the substrate binding site. Finally, conformational states of the substrate binding site with higher druggability scores than the crystal structure were identified. In summary, our study provides valuable insights into h-ecto-5'-NT structural flexibility, which can guide the structure-based design of novel h-ecto-5'-NT inhibitors.
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Affiliation(s)
- Lucas G Viviani
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany
| | - Antonia T-do Amaral
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
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das Neves GM, Kagami LP, Battastini AMO, Figueiró F, Eifler-Lima VL. Targeting ecto-5'-nucleotidase: A comprehensive review into small molecule inhibitors and expression modulators. Eur J Med Chem 2023; 247:115052. [PMID: 36599229 DOI: 10.1016/j.ejmech.2022.115052] [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: 10/20/2022] [Revised: 12/11/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023]
Abstract
The purinergic signaling has drawn attention from academia and more recently from pharmaceutical industries as a potential therapeutic route for cancer treatment, since ATP may act as chemotactic agent and possess in vitro antineoplastic activity. On the other way, adenosine, produced in extracellular medium by ecto-5'-NT, acts as immunosuppressor and is related to neoangiogenesis, vasculogenesis and evasion to the immune system. Consequently, inhibitors of ecto-5'-NT may prevent tumor progression, reducing adenosine concentrations, preventing escape from the host's immune system and slowing cancer's growth. This review aims to highlight important biochemical and structural features of ecto-5'NT, highlight its expression profile in normal and cancer cell lines detailing compounds which may act as expression regulators and to review the several classes of ecto-5'NT inhibitors developed in the past 12 years, in order to build a general structure-activity relationship model to guide further compound design.
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Affiliation(s)
- Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Maria Oliveira Battastini
- Laboratório de Imunobioquímica do Câncer (LIBC), Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fabrício Figueiró
- Laboratório de Imunobioquímica do Câncer (LIBC), Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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5
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Yegutkin GG, Boison D. ATP and Adenosine Metabolism in Cancer: Exploitation for Therapeutic Gain. Pharmacol Rev 2022; 74:797-822. [PMID: 35738682 DOI: 10.1124/pharmrev.121.000528] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Adenosine is an evolutionary ancient metabolic regulator linking energy state to physiologic processes, including immunomodulation and cell proliferation. Tumors create an adenosine-rich immunosuppressive microenvironment through the increased release of ATP from dying and stressed cells and its ectoenzymatic conversion into adenosine. Therefore, the adenosine pathway becomes an important therapeutic target to improve the effectiveness of immune therapies. Prior research has focused largely on the two major ectonucleotidases, ectonucleoside triphosphate diphosphohydrolase 1/cluster of differentiation (CD)39 and ecto-5'-nucleotidase/CD73, which catalyze the breakdown of extracellular ATP into adenosine, and on the subsequent activation of different subtypes of adenosine receptors with mixed findings of antitumor and protumor effects. New findings, needed for more effective therapeutic approaches, require consideration of redundant pathways controlling intratumoral adenosine levels, including the alternative NAD-inactivating pathway through the CD38-ectonucleotide pyrophosphatase phosphodiesterase (ENPP)1-CD73 axis, the counteracting ATP-regenerating ectoenzymatic pathway, and cellular adenosine uptake and its phosphorylation by adenosine kinase. This review provides a holistic view of extracellular and intracellular adenosine metabolism as an integrated complex network and summarizes recent data on the underlying mechanisms through which adenosine and its precursors ATP and ADP control cancer immunosurveillance, tumor angiogenesis, lymphangiogenesis, cancer-associated thrombosis, blood flow, and tumor perfusion. Special attention is given to differences and commonalities in the purinome of different cancers, heterogeneity of the tumor microenvironment, subcellular compartmentalization of the adenosine system, and novel roles of purine-converting enzymes as targets for cancer therapy. SIGNIFICANCE STATEMENT: The discovery of the role of adenosine as immune checkpoint regulator in cancer has led to the development of novel therapeutic strategies targeting extracellular adenosine metabolism and signaling in multiple clinical trials and preclinical models. Here we identify major gaps in knowledge that need to be filled to improve the therapeutic gain from agents targeting key components of the adenosine metabolic network and, on this basis, provide a holistic view of the cancer purinome as a complex and integrated network.
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Affiliation(s)
- Gennady G Yegutkin
- MediCity Research Laboratory and InFLAMES Flagship, University of Turku, Turku, Finland (G.G.Y.); Department of Neurosurgery, Robert Wood Johnson and New Jersey Medical Schools, Rutgers University, Piscataway, New Jersey (D.B.); and Rutgers Brain Health Institute, Piscataway, New Jersey (D.B.)
| | - Detlev Boison
- MediCity Research Laboratory and InFLAMES Flagship, University of Turku, Turku, Finland (G.G.Y.); Department of Neurosurgery, Robert Wood Johnson and New Jersey Medical Schools, Rutgers University, Piscataway, New Jersey (D.B.); and Rutgers Brain Health Institute, Piscataway, New Jersey (D.B.)
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6
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Liu X, Zhang Z, She N, Zhai J, Zhao Y, Wang C. Combination of multiple methods and views for recognition, transportation, and structure-guided modification of lysine-specific demethylase phenylcyclopropylamine inhibitor. Phys Chem Chem Phys 2022; 24:13806-13823. [PMID: 35612608 DOI: 10.1039/d2cp01197b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine-Specific Demethylase 1 (LSD1) is a typical histone-specific demethylase, which plays an important role in protein methylation modification. It is a member of the amine oxidase family (MAO) that specifically removes methyl groups from monomethylated H3K4, dimethylated H3K4 and H3K9 sites associated with tumorigenesis. Phenylcyclopropylamine derivatives are a class of specific LSD1 inhibitors, drawing attention due to their high efficiency. Here, extensive molecular dynamics (MD) simulations are combined with a three-dimensional quantitative structure-activity relationship (3D-QSAR) in order to design a new phenylcyclopropylamine inhibitor from multiple perspectives. In a ligand-oriented point of view, a 3D-QSAR model with comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) can be built based on the 55 phenylcyclopropylamine compounds targeting LSD1 obtained experimentally. The aromatic and piperazine rings are identified as the potential key groups regulating the activity of the compounds. In an interaction-oriented view, the representative compound is defined with the highest inhibitory efficiency. The binding and delivery mechanism and conformational dependence of activity, including channel and dynamic properties, are studied using RAMD and umbrella sampling technologies. The direct hydrogen bond and conjugated interactions are identified as a major driving force in this procedure. The dominant region of the phenylcyclopropylamine influences the free energy and detects the key residues in recognition and delivery. On the basis of both the ligand and interaction, a series of new inhibitor structures were designed, and two of them showed better efficiency. In order to select the inhibitor with a longer residence time, a comparison is conducted between the designed inhibitors and the experimentally obtained inhibitor from the perspective of static binding and dynamic delivery properties. This work creates new guidance for the phenylcyclopropylamine inhibitor design of LDS1 by combining the ligand and receptor, considering both static and dynamic properties. This scheme could be applied in other inhibitor design systems.
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Affiliation(s)
- Xiaoyuan Liu
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Zhiyang Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Jihang Zhai
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
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