1
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Parkins A, Pilien AVR, Wolff AM, Argueta C, Vargas J, Sadeghi S, Franz AH, Thompson MC, Pantouris G. The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes. J Med Chem 2024. [PMID: 38670943 DOI: 10.1021/acs.jmedchem.4c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Systematic analysis of molecular recognition is critical for understanding the biological function of macromolecules. For the immunomodulatory protein D-dopachrome tautomerase (D-DT), the mechanism of protein-ligand interactions is poorly understood. Here, 17 carefully designed protein variants and wild type (WT) D-DT were interrogated with an array of complementary techniques to elucidate the structural basis of ligand recognition. Utilization of a substrate and two selective inhibitors with distinct binding profiles offered previously unseen mechanistic insights into D-DT-ligand interactions. Our results demonstrate that the C-terminal region serves a key role in molecular recognition via regulation of the active site opening, protein-ligand interactions, and conformational flexibility of the pocket's environment. While our study is the first comprehensive analysis of molecular recognition for D-DT, the findings reported herein promote the understanding of protein functionality and enable the design of new structure-based drug discovery projects.
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Affiliation(s)
- Andrew Parkins
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | | | - Alexander M Wolff
- Department of Chemistry and Biochemistry, University of California, Merced, California 95340, United States
| | - Christopher Argueta
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Jasmine Vargas
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Shahrzad Sadeghi
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Andreas H Franz
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, California 95340, United States
| | - Georgios Pantouris
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
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2
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Jia X, Xi J, Tian B, Zhang Y, Wang Z, Wang F, Li Z, Long J, Wang J, Fan GH, Li Q. The Tautomerase Activity of Tumor Exosomal MIF Promotes Pancreatic Cancer Progression by Modulating MDSC Differentiation. Cancer Immunol Res 2024; 12:72-90. [PMID: 37956411 DOI: 10.1158/2326-6066.cir-23-0205] [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] [Received: 03/04/2023] [Revised: 07/28/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
Pancreatic cancer is a deadly disease that is largely resistant to immunotherapy, in part because of the accumulation of immunosuppressive cells in the tumor microenvironment (TME). Much evidence suggests that tumor-derived exosomes (TDE) contribute to the immunosuppressive activity mediated by myeloid-derived suppressor cells (MDSC) within the pancreatic cancer TME. However, the underlying mechanisms remain elusive. Herein, we report that macrophage migration inhibitory factor (MIF) in TDEs has a key role in inducing MDSC formation in pancreatic cancer. We identified MIF in both human and murine pancreatic cancer-derived exosomes. Upon specific shRNA-mediated knockdown of MIF, the ability of pancreatic cancer-derived exosomes to promote MDSC differentiation was abrogated. This phenotype was rescued by reexpression of the wild-type form of MIF rather than a tautomerase-null mutant or a thiol-protein oxidoreductase-null mutant, indicating that both MIF enzyme activity sites play a role in exosome-induced MDSC formation in pancreatic cancer. RNA sequencing data indicated that MIF tautomerase regulated the expression of genes required for MDSC differentiation, recruitment, and activation. We therefore developed a MIF tautomerase inhibitor, IPG1576. The inhibitor effectively inhibited exosome-induced MDSC differentiation in vitro and reduced tumor growth in an orthotopic pancreatic cancer model, which was associated with decreased numbers of MDSCs and increased infiltration of CD8+ T cells in the TME. Collectively, our findings highlight a pivotal role for MIF in exosome-induced MDSC differentiation in pancreatic cancer and underscore the potential of MIF tautomerase inhibitors to reverse the immunosuppressive pancreatic cancer microenvironment, thereby augmenting anticancer immune responses.
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Affiliation(s)
- Xuebing Jia
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianbei Xi
- Department of Medicinal Chemistry, Immunophage Biotech Co., Ltd., Shanghai, China
| | - Binle Tian
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanyuan Zhang
- Department of Oncology, Immunophage Biotech Co., Ltd., Shanghai, China
| | - Zhilong Wang
- Department of Oncology, Immunophage Biotech Co., Ltd., Shanghai, China
| | - Fan Wang
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Li
- Department of Autoimmune Disease, Immunophage Biotech Co., Ltd., Shanghai, China
| | - Jiang Long
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - JianFei Wang
- Excecutive Office, Immunophage Biotech Co., Ltd., Shanghai, China
- Shanghai Laboratory Animal Research Center, Shanghai, China
| | - Guo-Huang Fan
- Excecutive Office, Immunophage Biotech Co., Ltd., Shanghai, China
| | - Qi Li
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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3
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Chen E, Widjaja V, Kyro G, Allen B, Das P, Prahaladan VM, Bhandari V, Lolis EJ, Batista VS, Lisi GP. Mapping N- to C-terminal allosteric coupling through disruption of a putative CD74 activation site in D-dopachrome tautomerase. J Biol Chem 2023; 299:104729. [PMID: 37080391 PMCID: PMC10208890 DOI: 10.1016/j.jbc.2023.104729] [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: 12/16/2022] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
The macrophage migration inhibitory factor (MIF) protein family consists of MIF and D-dopachrome tautomerase (also known as MIF-2). These homologs share 34% sequence identity while maintaining nearly indistinguishable tertiary and quaternary structure, which is likely a major contributor to their overlapping functions, including the binding and activation of the cluster of differentiation 74 (CD74) receptor to mediate inflammation. Previously, we investigated a novel allosteric site, Tyr99, that modulated N-terminal catalytic activity in MIF through a "pathway" of dynamically coupled residues. In a comparative study, we revealed an analogous allosteric pathway in MIF-2 despite its unique primary sequence. Disruptions of the MIF and MIF-2 N termini also diminished CD74 activation at the C terminus, though the receptor activation site is not fully defined in MIF-2. In this study, we use site-directed mutagenesis, NMR spectroscopy, molecular simulations, in vitro and in vivo biochemistry to explore the putative CD74 activation region of MIF-2 based on homology to MIF. We also confirm its reciprocal structural coupling to the MIF-2 allosteric site and N-terminal enzymatic site. Thus, we provide further insight into the CD74 activation site of MIF-2 and its allosteric coupling for immunoregulation.
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Affiliation(s)
- Emily Chen
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Vinnie Widjaja
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Gregory Kyro
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Pragnya Das
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, New Jersey, USA
| | - Varsha M Prahaladan
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, New Jersey, USA
| | - Vineet Bhandari
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, New Jersey, USA
| | - Elias J Lolis
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, USA.
| | - George P Lisi
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA.
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4
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Parkins A, Chen E, Rangel VM, Singh M, Xue L, Lisi GP, Pantouris G. Ligand-induced conformational changes enable intersubunit communications in D-dopachrome tautomerase. Biophys J 2023; 122:1268-1276. [PMID: 36804669 PMCID: PMC10111345 DOI: 10.1016/j.bpj.2023.02.019] [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] [Received: 11/23/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
D-Dopachrome tautomerase (D-DT; or MIF-2) is a multifunctional protein with immunomodulatory properties and a documented pathogenic role in inflammation and cancer that is associated with activation of the cell surface receptor CD74. Alongside D-DT, macrophage migration inhibitory factor (MIF) is also known to activate CD74, promoting pathogenesis. While the role of the MIF/CD74 axis has been extensively studied in various disease models, the late discovery of the D-DT/CD74 axis has led to a poor investigation into the D-DT-induced activation mechanism of CD74. A previous study has identified 4-(3-carboxyphenyl)-2,5-pyridinedicarboxylic acid (4-CPPC) as the first selective and reversible inhibitor of D-DT and reported its potency to block the D-DT-induced activation of CD74 in a cell-based model. In this study, we employ molecular dynamics simulations and nuclear magnetic resonance experiments to study 4-CPPC-induced changes to the dynamic profile of D-DT. We found that binding of the inhibitor remarkably promotes the conformational flexibility of C-terminal without impacting the structural stability of the biological assembly. Consequently, long-range intrasubunit (>11 Å) and intersubunit (>30 Å) communications are enabled between distal regions. Communication across the three subunits is accomplished via 4-CPPC, which serves as a communication bridge after Val113 is displaced from its hydrophobic pocket. This previously unrecognized structural property of D-DT is not shared with its human homolog, MIF, which exhibits an impressive C-terminal rigidity even in the presence of an inhibitor. Considering the previously reported role of MIF's C-terminal in the activation of CD74, our results break new ground for understanding the functionality of D-DT in health and disease.
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Affiliation(s)
- Andrew Parkins
- Department of Chemistry, University of the Pacific, Stockton, California
| | - Emily Chen
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, Rhode Island
| | - Vanessa M Rangel
- Department of Chemistry, University of the Pacific, Stockton, California
| | - Mandeep Singh
- Department of Chemistry, University of the Pacific, Stockton, California
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, California
| | - George P Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, Rhode Island
| | - Georgios Pantouris
- Department of Chemistry, University of the Pacific, Stockton, California.
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5
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Parkins A, Sandin SI, Knittel J, Franz AH, Ren J, de Alba E, Pantouris G. Underrepresented Impurities in 4-Hydroxyphenylpyruvate Affect the Catalytic Activity of Multiple Enzymes. Anal Chem 2023; 95:4957-4965. [PMID: 36877482 DOI: 10.1021/acs.analchem.2c04969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a key immunostimulatory protein with regulatory properties in several disorders, including inflammation and cancer. All the reported inhibitors that target the biological activities of MIF have been discovered by testing against its keto/enol tautomerase activity. While the natural substrate is still unknown, model MIF substrates are used for kinetic experiments. The most extensively used model substrate is 4-hydroxyphenyl pyruvate (4-HPP), a naturally occurring intermediate of tyrosine metabolism. Here, we examine the impact of 4-HPP impurities in the precise and reproducible determination of MIF kinetic data. To provide unbiased evaluation, we utilized 4-HPP powders from five different manufacturers. Biochemical and biophysical analyses showed that the enzymatic activity of MIF is highly influenced by underrepresented impurities found in 4-HPP. Besides providing inconsistent turnover results, the 4-HPP impurities also influence the accurate calculation of ISO-1's inhibition constant, an MIF inhibitor that is broadly used for in vitro and in vivo studies. The macromolecular NMR data show that 4-HPP samples from different manufacturers result in differential chemical shift perturbations of amino acids in MIF's active site. Our MIF-based conclusions were independently evaluated and confirmed by 4-hydroxyphenylpyruvate dioxygenase (HPPD) and D-dopachrome tautomerase (D-DT); two additional enzymes that utilize 4-HPP as a substrate. Collectively, these results explain inconsistencies in previously reported inhibition values, highlight the effect of impurities on the accurate determination of kinetic parameters, and serve as a tool for designing error-free in vitro and in vivo experiments.
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Affiliation(s)
- Andrew Parkins
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Suzanne I Sandin
- Department of Bioengineering, University of California, Merced, California 95343, United States
- Chemistry and Biochemistry Graduate Program, University of California, Merced, California 95343, United States
| | - Jonathon Knittel
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Andreas H Franz
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Jianhua Ren
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Eva de Alba
- Department of Bioengineering, University of California, Merced, California 95343, United States
| | - Georgios Pantouris
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
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6
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Parkins A, Das P, Prahaladan V, Rangel VM, Xue L, Sankaran B, Bhandari V, Pantouris G. 2,5-Pyridinedicarboxylic acid is a bioactive and highly selective inhibitor of D-dopachrome tautomerase. Structure 2023; 31:355-367.e4. [PMID: 36805127 DOI: 10.1016/j.str.2023.01.008] [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: 11/10/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 02/19/2023]
Abstract
Macrophage migration inhibitory factor (MIF) and D-dopachrome tautomerase (D-DT) are two pleotropic cytokines, which are coexpressed in various cell types to activate the cell surface receptor CD74. Via the MIF/CD74 and D-DT/CD74 axes, the two proteins exhibit either beneficial or deleterious effect on human diseases. In this study, we report the identification of 2,5-pyridinedicarboxylic acid (a.k.a. 1) that effectively blocks the D-DT-induced activation of CD74 and demonstrates an impressive 79-fold selectivity for D-DT over MIF. Crystallographic characterization of D-DT-1 elucidates the binding features of 1 and reveals previously unrecognized differences between the MIF and D-DT active sites that explain the ligand's functional selectivity. The commercial availability, low cost, and high selectivity make 1 the ideal tool for studying the pathophysiological functionality of D-DT in disease models. At the same time, our comprehensive biochemical, computational, and crystallographic analyses serve as a guide for generating highly potent and selective D-DT inhibitors.
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Affiliation(s)
- Andrew Parkins
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA
| | - Pragnya Das
- Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper, Camden, NJ 08103, USA
| | - Varsha Prahaladan
- Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper, Camden, NJ 08103, USA
| | - Vanessa M Rangel
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, 1 Cyclotron Road, Lawrence Berkeley Nat. Lab, Berkeley, CA 94720, USA
| | - Vineet Bhandari
- Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper, Camden, NJ 08103, USA
| | - Georgios Pantouris
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA.
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7
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Skeens E, Gadzuk-Shea M, Shah D, Bhandari V, Schweppe DK, Berlow RB, Lisi GP. Redox-dependent structure and dynamics of macrophage migration inhibitory factor reveal sites of latent allostery. Structure 2022; 30:840-850.e6. [PMID: 35381187 DOI: 10.1016/j.str.2022.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 01/01/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a multifunctional immunoregulatory protein that is a key player in the innate immune response. Given its overexpression at sites of inflammation and in diseases marked by increasingly oxidative environments, a comprehensive understanding of how cellular redox conditions impact the structure and function of MIF is necessary. We used NMR spectroscopy and mass spectrometry to investigate biophysical signatures of MIF under varied solution redox conditions. Our results indicate that the MIF structure is modified and becomes increasingly dynamic in an oxidative environment, which may be a means to alter the MIF conformation and functional response in a redox-dependent manner. We identified latent allosteric sites within MIF through mutational analysis of redox-sensitive residues, revealing that a loss of redox-responsive residues attenuates CD74 receptor activation. Leveraging sites of redox sensitivity as targets for structure-based drug design therefore reveals an avenue to modulate MIF function in its "disease state."
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, USA
| | - Meagan Gadzuk-Shea
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dilip Shah
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, NJ 08103, USA
| | - Vineet Bhandari
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, NJ 08103, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rebecca B Berlow
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - George P Lisi
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, USA.
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8
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Cui JY, Lisi GP. Molecular Level Insights Into the Structural and Dynamic Factors Driving Cytokine Function. Front Mol Biosci 2021; 8:773252. [PMID: 34760929 PMCID: PMC8573031 DOI: 10.3389/fmolb.2021.773252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Cytokines are key mediators of cellular communication and regulators of biological advents. The timing, quantity and localization of cytokines are key features in producing specific biological outcomes, and thus have been thoroughly studied and reviewed while continuing to be a focus of the cytokine biology community. Due to the complexity of cellular signaling and multitude of factors that can affect signaling outcomes, systemic level studies of cytokines are ongoing. Despite their small size, cytokines can exhibit structurally promiscuous and dynamic behavior that plays an equally important role in biological activity. In this review using case studies, we highlight the recent insight gained from observing cytokines through a molecular lens and how this may complement a system-level understanding of cytokine biology, explain diversity of downstream signaling events, and inform therapeutic and experimental development.
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Affiliation(s)
- Jennifer Y Cui
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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