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Paurević M, Maršavelski A, Ivanković S, Stojković R, Ribić R. Di-mannosylation enhances the adjuvant properties of adamantane-containing desmuramyl peptides in vivo. Org Biomol Chem 2024; 22:6506-6519. [PMID: 38884368 DOI: 10.1039/d4ob00592a] [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: 06/18/2024]
Abstract
Muramyl dipeptide (MDP) is the smallest essential peptidoglycan substructure capable of promoting both innate and adaptive immune responses. Herein, we report on the design, synthesis, and in vivo study of the adjuvant properties of two novel MDP analogs containing an achiral adamantyl moiety attached to the desmuramyl dipeptide (DMP) pharmacophore and additionally modified by one mannosyl subunit (derivative 7) or two mannosyl subunits (derivative 11). Mannose substructures were introduced in order to assess how the degree of mannosylation affects the immune response and nucleotide-binding oligomerization-domain-containing protein 2 (NOD2) binding affinity, compared to the reference compound ManAdDMP. Both mannosylated MDP analogs showed improved immunomodulating properties, while the di-mannosylated derivative 11 displayed the highest, statistically significant increase in anti-OVA IgG production. In this study, for the first time, the di-mannosylated DMP derivative was synthesized and immunologically evaluated. Derivative 11 stimulates a Th-2-polarized type of immune reaction, similar to the reference compound ManAdDMP and MDP. Molecular dynamics (MD) simulations demonstrate that 11 has a higher NOD2 binding affinity than 7, indicating that introducing the second mannose significantly contributes to the binding affinity. Mannose interacts with key amino acid residues from the LRR hydrophobic pocket of the NOD2 receptor and loop 2.
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Affiliation(s)
- Marija Paurević
- Department of Chemistry, Josip Juraj Strossmayer University Osijek, HR-31000 Osijek, Croatia.
| | - Aleksandra Maršavelski
- Department of Chemistry, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia.
| | - Siniša Ivanković
- Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia.
| | - Ranko Stojković
- Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia.
| | - Rosana Ribić
- University Center Varaždin, University North, HR-42000 Varaždin, Croatia.
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2
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Choudhary R, Mahadevan R. FOCUS on NOD2: Advancing IBD Drug Discovery with a User-Informed Machine Learning Framework. ACS Med Chem Lett 2024; 15:1057-1070. [PMID: 39015268 PMCID: PMC11247655 DOI: 10.1021/acsmedchemlett.4c00148] [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: 04/02/2024] [Revised: 05/17/2024] [Accepted: 06/03/2024] [Indexed: 07/18/2024] Open
Abstract
In this study, we introduce the Framework for Optimized Customizable User-Informed Synthesis (FOCUS), a generative machine learning model tailored for drug discovery. FOCUS integrates domain expertise and uses Proximal Policy Optimization (PPO) to guide Monte Carlo Tree Search (MCTS) to efficiently explore chemical space. It generates SMILES representations of potential drug candidates, optimizing for druggability and binding efficacy to NOD2, PEP, and MCT1 receptors. The model is highly interpretive, allowing for user-feedback and expert-driven adjustments based on detailed cycle reports. Employing tools like SHAP and LIME, FOCUS provides a transparent analysis of decision-making processes, emphasizing features such as docking scores and interaction fingerprints. Comparative studies with Muramyl Dipeptide (MDP) demonstrate improved interaction profiles. FOCUS merges advanced machine learning with expert insight, accelerating the drug discovery pipeline.
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Affiliation(s)
- Ruhi Choudhary
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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3
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Adamson C, Liang Y, Feng S, Ng AWR, Qiao Y. A closer look at ligand specificity for cellular activation of NOD2 with synthetic muramyl dipeptide analogues. Chem Commun (Camb) 2024; 60:2212-2215. [PMID: 38305731 DOI: 10.1039/d3cc05807g] [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: 02/03/2024]
Abstract
To further understand the specificity of muramyl dipeptide (MDP) sensing by NOD2, we evaluated the compatibility of synthetic MDP analogues for cellular uptake and NAGK phosphorylation, the pre-requisite steps of intracellular NOD2 activation. Our results revealed that these two prior steps do not confer ligand stereoselectivity; yet NAGK strictly discriminates against the disaccharide NOD2 agonists for phosphorylation in vitro, despite it being indispensable for the cellular NOD2-stimulating effects of these analogues, implying potential glycosidase cleavage as a novel intermediate step for cellular activation of NOD2.
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Affiliation(s)
- Christopher Adamson
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), 21 Nanyang Link, 637371, Singapore.
| | - Yaquan Liang
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), 21 Nanyang Link, 637371, Singapore.
| | - Shiliu Feng
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), 21 Nanyang Link, 637371, Singapore.
| | - Allan Wee Ren Ng
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), 21 Nanyang Link, 637371, Singapore.
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), 21 Nanyang Link, 637371, Singapore.
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4
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Basu P, Das AA, Siddiqui KN, Mondal PC, Bandyopadhyay A. Novel role of peptidoglycan recognition protein 2 in activating NOD2-NFκB inflammatory axis in coronary artery disease. Atherosclerosis 2024; 389:117436. [PMID: 38277990 DOI: 10.1016/j.atherosclerosis.2023.117436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
BACKGROUNDS AND AIMS The role of inflammation in driving atherosclerosis is well-established. It exerts systemic effects beyond the local site of plaque formation. In the context of coronary artery disease (CAD), the proteins that show altered levels in the plasma, are potentially important for understanding the key regulatory mechanism in the pathogenesis of atherosclerosis. A case-control study revealed that plasma soluble Peptidoglycan Recognition Protein 2 (PGLYRP2) primarily produced by the liver, is increased in subjects with CAD. Furthermore, the concentration of PGLYRP2 in the blood correlates with the severity of coronary artery disease. Thus, it raises interest in understanding the exact role of the protein in aortic inflammation and plaque progression. METHODS We evaluated the plasma concentration of PGLYRP2 in three distinct groups: patients with CAD (N = 68), asymptomatic individuals (N = 34), and healthy volunteers (N = 20). Furthermore, we investigated the correlation between disease severity and PGLYRP2 levels in CAD patients. To identify potential binding partners of PGLYRP2, we employed computational analysis. We verified the PGLYRP2-NOD2 interaction in macrophage cells and elucidated the inflammatory pathways activated by PGLYRP2 within these cells. To assess the impact of PGLYRP2, we examined its effects in the atherosclerotic mice model (ApoE-/-). RESULTS In this study, we report for the first time that Nucleotide-binding Oligomerization domain 2 (NOD2) which is expressed on the surface of macrophages, is a receptor of PGLYRP2. The N-terminal domain of PGLYRP2 directly binds to NOD2 and activates the NOD2-RIP2-NFκB cascade that promotes the secretion of proinflammatory cytokines like TNFα, IL1β, and IL-8. In the atherosclerotic mice model (ApoE-/-) we demonstrate that elevated PGLYRP2 level is parallel with increased proinflammatory cytokines in the plasma when fed a High Cholesterol Diet (HCD). Immunohistochemical analysis reveals that PGLYRP2 is co-localized with NOD2 on the macrophages at the site of the lesion. CONCLUSIONS Taken together, our data demonstrate that NOD2 acts as a receptor of PGLYRP2 on macrophages, which mediates the activation of the NOD2-RIP2-NFκB pathway and promotes inflammation, thus significantly contributing to the development and progression of atherosclerosis.
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Affiliation(s)
- Pratitusti Basu
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, CN-6, Sector 5, Salt Lake, Kolkata, 700091, India
| | - Apabrita Ayan Das
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, CN-6, Sector 5, Salt Lake, Kolkata, 700091, India
| | | | | | - Arun Bandyopadhyay
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, CN-6, Sector 5, Salt Lake, Kolkata, 700091, India.
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5
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Tsukidate T, Hespen CW, Hang HC. Small molecule modulators of immune pattern recognition receptors. RSC Chem Biol 2023; 4:1014-1036. [PMID: 38033733 PMCID: PMC10685800 DOI: 10.1039/d3cb00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/03/2023] [Indexed: 12/02/2023] Open
Abstract
Pattern recognition receptors (PRRs) represent a re-emerging class of therapeutic targets for vaccine adjuvants, inflammatory diseases and cancer. In this review article, we summarize exciting developments in discovery and characterization of small molecule PRR modulators, focusing on Toll-like receptors (TLRs), NOD-like receptors (NLRs) and the cGAS-STING pathway. We also highlight PRRs that are currently lacking small molecule modulators and opportunities for chemical biology and therapeutic discovery.
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Affiliation(s)
- Taku Tsukidate
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York New York 10065 USA
| | - Charles W Hespen
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York New York 10065 USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York New York 10065 USA
- Department of Immunology and Microbiology and Department of Chemistry, Scripps Research, La Jolla California 92037 USA
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6
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Dixon CL, Wu A, Fairn GD. Multifaceted roles and regulation of nucleotide-binding oligomerization domain containing proteins. Front Immunol 2023; 14:1242659. [PMID: 37869013 PMCID: PMC10585062 DOI: 10.3389/fimmu.2023.1242659] [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: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
Nucleotide-binding oligomerization domain-containing proteins, NOD1 and NOD2, are cytosolic receptors that recognize dipeptides and tripeptides derived from the bacterial cell wall component peptidoglycan (PGN). During the past two decades, studies have revealed several roles for NODs beyond detecting PGN fragments, including activation of an innate immune anti-viral response, NOD-mediated autophagy, and ER stress induced inflammation. Recent studies have also clarified the dynamic regulation of NODs at cellular membranes to generate specific and balanced immune responses. This review will describe how NOD1 and NOD2 detect microbes and cellular stress and detail the molecular mechanisms that regulate activation and signaling while highlighting new evidence and the impact on inflammatory disease pathogenesis.
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Affiliation(s)
| | - Amy Wu
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Gregory D. Fairn
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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7
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Abstract
Mycobacteria are responsible for several human and animal diseases. NOD2 is a pattern recognition receptor that has an important role in mycobacterial recognition. However, the mechanisms by which mutations in NOD2 alter the course of mycobacterial infection remain unclear. Herein, we aimed to review the totality of studies directly addressing the relationship between NOD2 and mycobacteria as a foundation for moving the field forward. NOD2 was linked to mycobacterial infection at 3 levels: (1) genetic, through association with mycobacterial diseases of humans; (2) chemical, through the distinct NOD2 ligand in the mycobacterial cell wall; and (3) immunologic, through heightened NOD2 signaling caused by the unique modification of the NOD2 ligand. The immune response to mycobacteria is shaped by NOD2 signaling, responsible for NF-κB and MAPK activation, and the production of various immune effectors like cytokines and nitric oxide, with some evidence linking this to bacteriologic control. Absence of NOD2 during mycobacterial infection of mice can be detrimental, but the mechanism remains unknown. Conversely, the success of immunization with mycobacteria has been linked to NOD2 signaling and NOD2 has been targeted as an avenue of immunotherapy for diseases even beyond mycobacteria. The mycobacteria-NOD2 interaction remains an important area of study, which may shed light on immune mechanisms in disease.
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Affiliation(s)
- Jean-Yves Dubé
- Department of Microbiology and Immunology, McGill University, Montréal, Canada
| | - Marcel A Behr
- Department of Medicine, McGill University Health Centre, Montréal, Canada
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8
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Novel Scaffolds for Modulation of NOD2 Identified by Pharmacophore-Based Virtual Screening. Biomolecules 2022; 12:biom12081054. [PMID: 36008948 PMCID: PMC9405794 DOI: 10.3390/biom12081054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 12/04/2022] Open
Abstract
Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is an innate immune pattern recognition receptor responsible for the recognition of bacterial peptidoglycan fragments. Given its central role in the formation of innate and adaptive immune responses, NOD2 represents a valuable target for modulation with agonists and antagonists. A major challenge in the discovery of novel small-molecule NOD2 modulators is the lack of a co-crystallized complex with a ligand, which has limited previous progress to ligand-based design approaches and high-throughput screening campaigns. To that end, a hybrid docking and pharmacophore modeling approach was used to identify key interactions between NOD2 ligands and residues in the putative ligand-binding site. Following docking of previously reported NOD2 ligands to a homology model of human NOD2, a structure-based pharmacophore model was created and used to virtually screen a library of commercially available compounds. Two compounds, 1 and 3, identified as hits by the pharmacophore model, exhibited NOD2 antagonist activity and are the first small-molecule NOD2 modulators identified by virtual screening to date. The newly identified NOD2 antagonist scaffolds represent valuable starting points for further optimization.
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9
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Hespen CW, Zhao X, Hang HC. Membrane targeting enhances muramyl dipeptide binding to NOD2 and Arf6-GTPase in mammalian cells. Chem Commun (Camb) 2022; 58:6598-6601. [PMID: 35584401 DOI: 10.1039/d2cc01903e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To further understand the mechanisms of muramyl dipeptide (MDP) sensing by NOD2, we evaluated key properties involved in the formation of the Arf6-MDP-NOD2 complex in mammalian cells. We found that the conserved Arf aromatic triad is crucial for binding to MDP-NOD2. Mutation of Arf6 N-myristoylation and NOD2 S-palmitoylation also abrogated the formation of the Arf6-MDP-NOD2 complex. Notably, lipid-modified MDP (L18-MDP) increased Arf6-NOD2 assembly. Our results indicate recruitment of Arf6 may explain enhanced activity of lipidated MDP analogues and membrane targeting may be important in developing next-generation NOD2 agonists.
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Affiliation(s)
- Charles W Hespen
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
| | - Xiaohui Zhao
- Department of Immunology and Microbiology and Department of Chemistry, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Howard C Hang
- Department of Immunology and Microbiology and Department of Chemistry, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
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10
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Le HT, D’Ambrosio EA, Mashayekh S, Grimes CL. Customized peptidoglycan surfaces to investigate innate immune recognition via surface plasmon resonance. Methods Enzymol 2022; 665:73-103. [PMID: 35379444 PMCID: PMC9042648 DOI: 10.1016/bs.mie.2021.12.004] [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: 01/16/2023]
Abstract
Glycan-protein interactions facilitate some of the most important biomolecular processes in and between cells. They are involved in different cellular pathways, cell-cell interactions and associated with many diseases, making these interactions of great interest. However, their structural and functional diversity poses great challenges in studying them at the molecular level. Surface plasmon resonance (SPR) technology presents great advantages to study glycan-protein interactions due to its superior sensitivity, ability to monitor real-time interactions, relatively simple data interpretation, and most importantly, direct measurement of binding without a need for fluorescent labeling. Here, another dimensionality of SPR in studying glycan-protein interactions is demonstrated via examples of binding between human innate immune receptors and their bacterial peptidoglycan ligands. In order to best resemble interactions in solution, a novel strategy of tethering the carbohydrate at different positions to the biosensor surface is applied to represent the potential displays of the carbohydrate ligand to the receptor. Subsequent kinetic analysis provides insights into the optimized configuration of peptidoglycan fragments for binding with its receptors. The manuscript contains a "how-to guide" to help with the implementation of these methods in other glycan-protein binding systems.
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Affiliation(s)
- Ha T. Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Elizabeth A. D’Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States,Correspondence to Catherine L. Grimes, The University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716,
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11
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Brown AR, Wodzanowski KA, Santiago CC, Hyland SN, Follmar JL, Asare-Okai P, Grimes CL. Protected N-Acetyl Muramic Acid Probes Improve Bacterial Peptidoglycan Incorporation via Metabolic Labeling. ACS Chem Biol 2021; 16:1908-1916. [PMID: 34506714 DOI: 10.1021/acschembio.1c00268] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metabolic glycan probes have emerged as an excellent tool to investigate vital questions in biology. Recently, methodology to incorporate metabolic bacterial glycan probes into the cell wall of a variety of bacterial species has been developed. In order to improve this method, a scalable synthesis of the peptidoglycan precursors is developed here, allowing for access to essential peptidoglycan immunological fragments and cell wall building blocks. The question was asked if masking polar groups of the glycan probe would increase overall incorporation, a common strategy exploited in mammalian glycobiology. Here, we show, through cellular assays, that E. coli do not utilize peracetylated peptidoglycan substrates but do employ methyl esters. The 10-fold improvement of probe utilization indicates that (i) masking the carboxylic acid is favorable for transport and (ii) bacterial esterases are capable of removing the methyl ester for use in peptidoglycan biosynthesis. This investigation advances bacterial cell wall biology, offering a prescription on how to best deliver and utilize bacterial metabolic glycan probes.
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Affiliation(s)
- Ashley R. Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Kimberly A. Wodzanowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Cintia C. Santiago
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Stephen N. Hyland
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Julianna L. Follmar
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - PapaNii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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12
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Bersch K, DeMeester KE, Zagani R, Chen S, Wodzanowski KA, Liu S, Mashayekh S, Reinecker HC, Grimes CL. Bacterial Peptidoglycan Fragments Differentially Regulate Innate Immune Signaling. ACS CENTRAL SCIENCE 2021; 7:688-696. [PMID: 34056099 PMCID: PMC8155477 DOI: 10.1021/acscentsci.1c00200] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 05/07/2023]
Abstract
The human innate immune system responds to both pathogen and commensal bacteria at the molecular level using bacterial peptidoglycan (PG) recognition elements. Traditionally, synthetic and commercially accessible PG monosaccharide units known as muramyl dipeptide (MDP) and N-glycolyl MDP (ng-MDP) have been used to probe the mechanism of innate immune activation of pattern recognition receptors, such as NOD-like receptors. However, bacterial PG is a dynamic and complex structure, with various chemical modifications and trimming mechanisms that result in the production of disaccharide-containing elements. These molecules pose as attractive targets for immunostimulatory screening; however, studies are limited because of their synthetic accessibility. Inspired by disaccharide-containing compounds produced from the gut microbe Lactobacillus acidophilus, a robust and scalable chemical synthesis of PG-based disaccharide ligands was implemented. Together with a monosaccharide PG library, compounds were screened for their ability to stimulate proinflammatory genes in bone-marrow-derived macrophages. The data reveal distinct gene induction patterns for monosaccharide and disaccharide PG units, suggesting that PG innate immune signaling is more complex than a one activator-one pathway program, as biologically relevant fragments induce transcriptional programs to different degrees. These disaccharide molecules will serve as critical immunostimulatory tools to more precisely define specialized innate immune regulatory mechanisms that distinguish between commensal and pathogenic bacteria residing in the microbiome.
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Affiliation(s)
- Klare
L. Bersch
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Kristen E. DeMeester
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Rachid Zagani
- Department
of Medicine, Gastrointestinal Unit and Center for the Study of Inflammatory
Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shuyuan Chen
- Department
of Medicine, Division of Digestive and Liver Diseases, and Department
of Immunology, University of Texas Southwestern
Medical Center, 5959 Harry Hines Boulevard, Dallas, Texas 75390, United
States
| | - Kimberly A. Wodzanowski
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Shuzhen Liu
- Department
of Medicine, Division of Digestive and Liver Diseases, and Department
of Immunology, University of Texas Southwestern
Medical Center, 5959 Harry Hines Boulevard, Dallas, Texas 75390, United
States
| | - Siavash Mashayekh
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Hans-Christian Reinecker
- Department
of Medicine, Gastrointestinal Unit and Center for the Study of Inflammatory
Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department
of Medicine, Division of Digestive and Liver Diseases, and Department
of Immunology, University of Texas Southwestern
Medical Center, 5959 Harry Hines Boulevard, Dallas, Texas 75390, United
States
| | - Catherine L. Grimes
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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13
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Kim CS, Brown AM, Grove TZ, Etzkorn FA. Designed leucine-rich repeat proteins bind two muramyl dipeptide ligands. Protein Sci 2021; 30:804-817. [PMID: 33512005 DOI: 10.1002/pro.4031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 12/15/2022]
Abstract
Designed protein receptors hold diagnostic and therapeutic promise. We now report the design of five consensus leucine-rich repeat proteins (CLRR4-8) based on the LRR domain of nucleotide-binding oligomerization domain (NOD)-like receptors involved in the innate immune system. The CLRRs bind muramyl dipeptide (MDP), a bacterial cell wall component, with micromolar affinity. The overall Kd app values ranged from 1.0 to 57 μM as measured by fluorescence quenching experiments. Biphasic fluorescence quenching curves were observed in all CLRRs, with higher affinity Kd1 values ranging from 0.04 to 4.5 μM, and lower affinity Kd2 values ranging from 3.1 to 227 μM. These biphasic binding curves, along with the docking studies of MDP binding to CLRR4, suggest that at least two MDPs bind to each protein. Previously, only single MDP binding was reported. This high-capacity binding of MDP promises small, soluble, stable CLRR scaffolds as candidates for the future design of pathogen biosensors.
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Affiliation(s)
- Christina S Kim
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Anne M Brown
- University Libraries, Virginia Tech, Blacksburg, Virginia, USA
| | - Tijana Z Grove
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, USA
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14
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Crump GM, Zhou J, Mashayekh S, Grimes CL. Revisiting peptidoglycan sensing: interactions with host immunity and beyond. Chem Commun (Camb) 2020; 56:13313-13322. [PMID: 33057506 PMCID: PMC7642115 DOI: 10.1039/d0cc02605k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interaction between host immunity and bacterial cells plays a pivotal role in a variety of human diseases. The bacterial cell wall component peptidoglycan (PG) is known to stimulate an immune response, which makes PG a distinctive recognition element for unveiling these complicated molecular interactions. Pattern recognition receptor (PRR) proteins are among the critical components of this system that initially recognize molecular patterns associated with microorganisms such as bacteria and fungi. These molecular patterns are mostly embedded in the bacterial or fungal cell wall structure and can be released and presented to the immune system in various situations. Nonetheless, detailed knowledge of this recognition is limited due to the diversity among the PG polymer and its fragments; the subsequent responses by multiple hosts add more complexity. Here, we discuss how our understanding of the role and molecular mechanisms of the well-studied PRR, the NOD-like receptors (NLRs), in the human immune system has evolved in recent years. We highlight the instances of other classes of proteins with similar behavior in the recognition of PG that have been identified in other microorganisms such as yeasts. These proteins are particularly interesting because a network of cellular interactions exists between human host cells, bacteria and yeast as a part of the normal human flora. To support our understanding of these interactions, we provide insight into the chemist's toolbox of peptidoglycan probes that aid in the investigations of the behaviors of these proteins and other biological contexts relevant to the sensing and recognition of peptidoglycan. The importance of these interactions in human health for the development of biomarkers and biotherapy is highlighted.
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Affiliation(s)
- Geneva Maddison Crump
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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15
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Mashayekh S, Bersch KL, Ramsey J, Harmon T, Prather B, Genova LA, Grimes CL. Synthesis of Bacterial-Derived Peptidoglycan Cross-Linked Fragments. J Org Chem 2020; 85:16243-16253. [PMID: 33108204 DOI: 10.1021/acs.joc.0c01852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptidoglycan (PG) is the core structural motif of the bacterial cell wall. Fragments released from the PG serve as fundamental recognition elements for the immune system. The structure of the PG, however, encompasses a variety of chemical modifications among different bacterial species. Here, the applicability of organic synthetic methods to address this chemical diversity is explored, and the synthesis of cross-linked PG fragments, carrying biologically relevant amino acid modifications and peptide cross-linkages, is presented using solution and solid phase approaches.
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Affiliation(s)
- Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Klare L Bersch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jared Ramsey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Thomas Harmon
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Benjamin Prather
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Lauren A Genova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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16
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D’Ambrosio EA, Bersch KL, Lauro ML, Grimes CL. Differential Peptidoglycan Recognition Assay Using Varied Surface Presentations. J Am Chem Soc 2020; 142:10926-10930. [PMID: 32520538 PMCID: PMC7601999 DOI: 10.1021/jacs.0c03933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial peptidoglycan (PG) is recognized by the human innate immune system to generate an appropriate response. To gain an appreciation of how this essential polymer is sensed, a surface plasmon resonance (SPR) assay using varied PG surface presentation was developed. PG derivatives were synthesized and immobilized on the surface at different positions on the molecule to assess effects of ligand orientation on the binding affinities of NOD-like receptors (NLRs). NLRP1 and NOD2 are cytosolic innate immune proteins known to generate an immune response to PG. Both possess conserved leucine rich repeat domains (LRR) as proposed sites of molecular recognition, though limited biochemical evidence exists regarding the mechanisms of PG recognition. Here direct biochemical evidence for the association of PG fragments to NOD2 and NLRP1 with nanomolar affinity is shown. The orientations in which the fragments were presented on the SPR surface influenced the strength of PG recognition by both NLRs. This assay displays fundamental differences in binding preferences for PG by innate immune receptors and reveals unique recognition mechanisms between the LRRs. Each receptor uses specific ligand structural features to achieve optimal binding, which will be critical information to manipulate these responses and combat diseases.
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Affiliation(s)
| | - Klare L. Bersch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Mackenzie L. Lauro
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Department of Biological Sciences, University of Delaware, Newark, DE 19716
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17
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Ukaegbu OI, DeMeester KE, Liang H, Brown AR, Jones ZS, Grimes CL. Utility of bacterial peptidoglycan recycling enzymes in the chemoenzymatic synthesis of valuable UDP sugar substrates. Methods Enzymol 2020; 638:1-26. [PMID: 32416908 DOI: 10.1016/bs.mie.2020.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Uridine diphosphate (UDP) sugars are essential precursors for glycosylation reactions in all forms of life. Reactions that transfer the carbohydrate from the UDP donor are catalyzed by glycosyltransferases (Gtfs). While the stereochemistry and negative physiological charge of UDP-sugars are essential for their biochemical function in the cell, these characteristics make them challenging molecules to synthesize and purify on scale in the laboratory. This chapter focuses on the utilization of a chemoenzymatic synthesis of muramyl UDP-sugars, key building blocks in the bacterial cell peptidoglycan. A scalable strategy to obtain UDP-N-acetyl muramic acid derivatives (UDP-NAM), the first committed intermediate used solely in peptidoglycan biosynthesis, is described herein. This methodology utilizes two enzymes involving the cell wall recycling enzymes MurNAc/GlcNAc anomeric kinase (AmgK) and NAM α-1-phosphate uridylyl transferase (MurU), respectively. The promiscuity of these enzymes allows for the unique chemical functionality to be embedded in bacterial peptidoglycan both in vitro and in whole bacterial cells for subsequent structural and functional studies of this important biopolymer.
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Affiliation(s)
- Ophelia I Ukaegbu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Ashley R Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Zachary S Jones
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States.
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18
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Zhang J, He J, Li J, Zhou Q, Chen H, Zheng Z, Chen Q, Chen D, Chen J. The immunogenicity and protective immunity of multi-epitopes DNA prime-protein boost vaccines encoding Amastin-Kmp-11, Kmp11-Gp63 and Amastin-Gp63 against visceral leishmaniasis. PLoS One 2020; 15:e0230381. [PMID: 32176727 PMCID: PMC7075555 DOI: 10.1371/journal.pone.0230381] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/28/2020] [Indexed: 11/27/2022] Open
Abstract
Visceral leishmaniasis (VL) is the most fatal form of leishmaniasis if left untreated and 50,000 to 90,000 new cases of VL occur worldwide each year. Although various vaccines had been studied in animal models, none of them was eligible to prevent human from infections. In this study, according to the silico analysis of Leishmania Amastin, Kmp-11 and Gp63 protein, dominant epitope sequences of these proteins were selected and linked to construct dominant multi-epitopes DNA and protein vaccines (Amastin-Kmp-11, Amastin-Gp63 and Kmp-11-Gp63) against VL. BALB/c mice were immunized with a DNA prime-protein boost immunization strategy and challenged with a new Leishmania parasite strain isolated from a VL patient. After immunization, the results including specific antibody titers, IL-4 and TNF-α levels, and CD4 and CD8 T cell proportion suggested the potent immunogenicity of the three vaccines. After infection, the results of spleen parasite burdens in the three vaccine groups were significantly lower than those of control groups, and the parasite reduction rates of Amastin-Kmp-11, Amastin-Gp63 and Kmp-11-Gp63 groups were 89.38%, 91.01% and 88.42%, respectively. Spleen smear observation and liver histopathological changes showed that all vaccine groups could produce significant immunoprotection against VL and Amastin-Gp63 vaccine was the best. In conclusion, our work demonstrated that the three dominant multi-epitopes Amastin-Kmp-11, Amastin-Gp63 and Kmp-11-Gp63 DNA prime-protein boost vaccines might be new vaccine candidates for VL, and the Amastin-Gp63 vaccine have best efficacy.
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Affiliation(s)
- Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jinlei He
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qi Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Han Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qiwei Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, Sichuan, China
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19
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Thiem K, Hoeke G, Zhou E, Hijmans A, Houben T, Boels MG, Mol IM, Lutgens E, Shiri-Sverdlov R, Bussink J, Kanneganti TD, Boon MR, Stienstra R, Tack CJ, Rensen PCN, Netea MG, Berbée JFP, van Diepen JA. Deletion of haematopoietic Dectin-2 or CARD9 does not protect from atherosclerosis development under hyperglycaemic conditions. Diab Vasc Dis Res 2020; 17:1479164119892140. [PMID: 31868000 PMCID: PMC7510497 DOI: 10.1177/1479164119892140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND C-type lectin receptors, including Dectin-2, are pattern recognition receptors on monocytes and macrophages that mainly recognize sugars and sugar-like structures present on fungi. Activation of C-type lectin receptors induces downstream CARD9 signalling, leading to the production of cytokines. We hypothesized that under hyperglycaemic conditions, as is the case in diabetes mellitus, glycosylated protein (sugar-like) structures activate C-type lectin receptors, leading to immune cell activation and increased atherosclerosis development. METHODS Low-density lipoprotein receptor-deficient mice were lethally irradiated and transplanted with bone marrow from control wild-type, Dectin-2-/- or Card9-/- mice. After 6 weeks of recovery, mice received streptozotocin injections (50 mg/g BW; 5 days) to induce hyperglycaemia. After an additional 2 weeks, mice were fed a Western-type diet (0.1% cholesterol) for 10 weeks. RESULTS AND CONCLUSION Deletion of haematopoietic Dectin-2 reduced the number of circulating Ly6Chi monocytes, increased pro-inflammatory cytokine production, but did not affect atherosclerosis development. Deletion of haematopoietic CARD9 tended to reduce macrophage and collagen content in atherosclerotic lesions, again without influencing the lesion size. Deletion of haematopoietic Dectin-2 did not influence atherosclerosis development under hyperglycaemic conditions, despite some minor effects on inflammation. Deletion of haematopoietic CARD9 induced minor alterations in plaque composition under hyperglycaemic conditions, without affecting lesion size.
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MESH Headings
- Animals
- Antigens, Ly/metabolism
- Aorta/metabolism
- Aorta/pathology
- Aortic Diseases/etiology
- Aortic Diseases/genetics
- Aortic Diseases/metabolism
- Aortic Diseases/pathology
- Atherosclerosis/etiology
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Biomarkers/blood
- Blood Glucose/metabolism
- Bone Marrow Transplantation
- CARD Signaling Adaptor Proteins/deficiency
- CARD Signaling Adaptor Proteins/genetics
- Cells, Cultured
- Collagen/metabolism
- Cytokines/metabolism
- Diabetes Mellitus, Experimental/blood
- Diabetes Mellitus, Experimental/complications
- Diet, Western
- Gene Deletion
- Genetic Predisposition to Disease
- Hematopoietic Stem Cells/metabolism
- Lectins, C-Type/deficiency
- Lectins, C-Type/genetics
- Macrophages, Peritoneal/metabolism
- Macrophages, Peritoneal/pathology
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Monocytes/metabolism
- Monocytes/pathology
- Plaque, Atherosclerotic
- Receptors, LDL/deficiency
- Receptors, LDL/genetics
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Affiliation(s)
- Kathrin Thiem
- Department of Internal Medicine and
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center,
Nijmegen, The Netherlands
- Kathrin Thiem, Department of Internal
Medicine and Radboud Institute for Molecular Life Sciences, Radboud University
Medical Center, 463, Geert Grooteplein zuid 8, 6525 GA Nijmegen, The
Netherlands.
| | - Geerte Hoeke
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental
Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Enchen Zhou
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental
Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Anneke Hijmans
- Department of Internal Medicine and
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center,
Nijmegen, The Netherlands
| | - Tom Houben
- Departments of Molecular Genetics, Human
Biology and Surgery, School of Nutrition and Translational Research in Metabolism
(NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Margien G Boels
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Division of Nephrology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Isabel M Mol
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental
Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Esther Lutgens
- Division of Experimental Vascular
Biology, Department of Medical Biochemistry, Academic Medical Center, University of
Amsterdam, Amsterdam, The Netherlands
- Institute for Cardiovascular Prevention,
Ludwig Maximilians University of Munich, Munich, Germany
| | - Ronit Shiri-Sverdlov
- Departments of Molecular Genetics, Human
Biology and Surgery, School of Nutrition and Translational Research in Metabolism
(NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Johan Bussink
- Department of Radiation Oncology,
Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Mariëtte R Boon
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental
Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Rinke Stienstra
- Department of Internal Medicine and
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center,
Nijmegen, The Netherlands
- Division of Human Nutrition,
Wageningen University, Wageningen, The Netherlands
| | - Cees J Tack
- Department of Internal Medicine and
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center,
Nijmegen, The Netherlands
| | - Patrick CN Rensen
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental
Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center,
Nijmegen, The Netherlands
- Department for Genomics and
Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn,
Bonn, Germany
| | - Jimmy FP Berbée
- Division of Endocrinology, Department of
Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental
Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Janna A van Diepen
- Department of Internal Medicine and
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center,
Nijmegen, The Netherlands
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20
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Kufer TA, Creagh EM, Bryant CE. Guardians of the Cell: Effector-Triggered Immunity Steers Mammalian Immune Defense. Trends Immunol 2019; 40:939-951. [PMID: 31500957 DOI: 10.1016/j.it.2019.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/31/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
The mammalian innate immune system deals with invading pathogens and stress by activating pattern-recognition receptors (PRRs) in the host. Initially proposed to be triggered by the discrimination of defined molecular signatures from pathogens rather than from self, it is now clear that PRRs can also be activated by endogenous ligands, bacterial metabolites and, following pathogen-induced alterations of cellular processes, changes in the F-actin cytoskeleton. These processes are collectively referred to as effector-triggered immunity (ETI). Here, we summarize the molecular and conceptual advances in our understanding of cell autonomous innate immune responses against bacterial pathogens, and discuss how classical activation of PRRs and ETI interplay to drive inflammatory responses.
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Affiliation(s)
- Thomas A Kufer
- Institute of Nutritional Medicine, Department of Immunology, University of Hohenheim, Stuttgart, Germany.
| | - Emma M Creagh
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.
| | - Clare E Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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21
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Brott AS, Clarke AJ. Peptidoglycan O-Acetylation as a Virulence Factor: Its Effect on Lysozyme in the Innate Immune System. Antibiotics (Basel) 2019; 8:E94. [PMID: 31323733 PMCID: PMC6783866 DOI: 10.3390/antibiotics8030094] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/11/2019] [Accepted: 07/13/2019] [Indexed: 11/16/2022] Open
Abstract
The peptidoglycan sacculus of both Gram-positive and Gram-negative bacteria acts as a protective mesh and provides structural support around the entirety of the cell. The integrity of this structure is of utmost importance for cell viability and so naturally is the first target for attack by the host immune system during bacterial infection. Lysozyme, a muramidase and the first line of defense of the innate immune system, targets the peptidoglycan sacculus hydrolyzing the β-(1→4) linkage between repeating glycan units, causing lysis and the death of the invading bacterium. The O-acetylation of N-acetylmuramoyl residues within peptidoglycan precludes the productive binding of lysozyme, and in doing so renders it inactive. This modification has been shown to be an important virulence factor in pathogens such as Staphylococcus aureus and Neisseria gonorrhoeae and is currently being investigated as a novel target for anti-virulence therapies. This article reviews interactions made between peptidoglycan and the host immune system, specifically with respect to lysozyme, and how the O-acetylation of the peptidoglycan interrupts these interactions, leading to increased pathogenicity.
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Affiliation(s)
- Ashley S Brott
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Anthony J Clarke
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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22
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D'Ambrosio EA, Drake WR, Mashayekh S, Ukaegbu OI, Brown AR, Grimes CL. Modulation of the NOD-like receptors NOD1 and NOD2: A chemist's perspective. Bioorg Med Chem Lett 2019; 29:1153-1161. [PMID: 30890292 PMCID: PMC7679954 DOI: 10.1016/j.bmcl.2019.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022]
Abstract
The innate immune system is the body's first defense against invading microorganisms, relying on the recognition of bacterial-derived small molecules by host protein receptors. This recognition event and downstream immune response rely heavily on the specific chemical features of both the innate immune receptors and their bacterial derived ligands. This review presents a chemist's perspective on some of the most crucial and complex components of two receptors (NOD1 and NOD2): starting from the structural and chemical characteristics of bacterial-derived small molecules, to the specific proposed models of molecular recognition of these molecules by immune receptors, to the subsequent post-translational modifications that ultimately dictate downstream immune signaling. Recent advances in the field are discussed, as well as the potential for the development of targeted therapeutics.
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Affiliation(s)
| | - Walter R Drake
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ophelia I Ukaegbu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ashley R Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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23
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Lazor KM, Zhou J, DeMeester KE, D'Ambrosio EA, Grimes CL. Synthesis and Application of Methyl N,O-Hydroxylamine Muramyl Peptides. Chembiochem 2019; 20:1369-1375. [PMID: 30672111 DOI: 10.1002/cbic.201800731] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 01/01/2023]
Abstract
The innate immune system's interaction with bacterial cells plays a pivotal role in a variety of human diseases. Carbohydrate units derived from a component of bacterial cell wall, peptidoglycan (PG), are known to stimulate an immune response. Nonetheless, access to modified late-stage peptidoglycan intermediates is limited due to their synthetic complexity. A method to rapidly functionalize PG fragments is needed to better understand the natural host-PG interactions. Here methyl N,O-hydroxylamine linkers are incorporated onto a synthetic PG derivative, muramyl dipeptide (MDP). The modification of MDP maintained the ability to stimulate a nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) immune response dependent on the expression of nucleotide-binding oligomerization domain-containing protein 2 (Nod2). Intrigued by this modification's maintenance of biological activity, several applications were explored. Methyl N,O-hydroxylamine MDP was amendable to N-hydroxylsuccinimide (NHS) chemistry for bioconjugation to fluorophores as well as a self-assembled monolayer for Nod2 surface plasmon resonance analysis. Finally, linker incorporation was applicable to larger PG fragments, both enzymatically generated from Escherichia coli or chemically synthesized. This methodology provides rapid access to PG probes in one step and allows for the installation of a variety of chemical handles to advance the molecular understanding of PG and the innate immune system.
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Affiliation(s)
- Klare M Lazor
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Junhui Zhou
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Elizabeth A D'Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA.,Department of Biological Sciences, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
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24
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Wang YC, Westcott NP, Griffin ME, Hang HC. Peptidoglycan Metabolite Photoaffinity Reporters Reveal Direct Binding to Intracellular Pattern Recognition Receptors and Arf GTPases. ACS Chem Biol 2019; 14:405-414. [PMID: 30735346 DOI: 10.1021/acschembio.8b01038] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The peptidoglycan fragments γ-d-glutamyl- meso-diaminopimelic acid (iE-DAP) and muramyl-dipeptide (MDP) are microbial-specific metabolites that activate intracellular pattern recognition receptors and stimulate immune signaling pathways. While extensive structure-activity studies have demonstrated that these bacterial cell wall metabolites trigger NOD1- and NOD2-dependent signaling, their direct binding to these innate immune receptors or other proteins in mammalian cells has not been established. To characterize these fundamental microbial metabolite-host interactions, we synthesized a series of peptidoglycan metabolite photoaffinity reporters and evaluated their cross-linking to NOD1 and NOD2 in mammalian cells. We show that active iE-DAP and MDP photoaffinity reporters selectively cross-linked NOD1 and NOD2, respectively, and not their inactive mutants. We also discovered MDP reporter cross-linking to Arf GTPases, which interacted most prominently with GTP-bound Arf6 and coimmunoprecipitated with NOD2 upon MDP stimulation. Notably, MDP binding to NOD2 and Arf6 was abrogated with loss-of-function NOD2 mutants associated with Crohn's disease. Our studies demonstrate peptidoglycan metabolite photoaffinity reporters can capture their cognate immune receptors in cells and reveal unpredicted ligand-induced interactions with other cellular cofactors. These photoaffinity reporters should afford useful tools to discover and characterize other peptidoglycan metabolite-interacting proteins.
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Affiliation(s)
- Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Nathan P. Westcott
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Matthew E. Griffin
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
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25
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Burch JM, Mashayekh S, Wykoff DD, Grimes CL. Bacterial Derived Carbohydrates Bind Cyr1 and Trigger Hyphal Growth in Candida albicans. ACS Infect Dis 2018; 4:53-58. [PMID: 29040806 PMCID: PMC5800403 DOI: 10.1021/acsinfecdis.7b00154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The dimorphic yeast Candida albicans is the most common pathogenic fungus found in humans. While this species is normally commensal, a morphological switch from budding yeast to filamentous hyphae allows the fungi to invade epithelial cells and cause infections. The phenotypic change is controlled by the adenylyl cyclase, Cyr1. Interestingly, this protein contains a leucine-rich repeat (LRR) domain, which is commonly found in innate immune receptors from plants and animals. A functional and pure LRR domain was obtained in high yields from E. coli expression. Utilizing a surface plasmon resonance assay, the LRR was found to bind diverse bacterial derived carbohydrates with high affinity. This domain is capable of binding fragments of peptidoglycan, a carbohydrate polymer component of the bacterial cell wall, as well as anthracyclines produced by Streptomyces, leading to hyphae formation. These findings add another dimension to the human microbiome, taking into account yeast-bacteria interactions that occur in the host.
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Affiliation(s)
- Jason M. Burch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Dennis D. Wykoff
- Department of Biology, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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Schaefer AK, Wastyk HC, Mohanan V, Hou CW, Lauro ML, Melnyk JE, Burch JM, Grimes CL. Crohn's Disease Variants of Nod2 Are Stabilized by the Critical Contact Region of Hsp70. Biochemistry 2017; 56:4445-4448. [PMID: 28792733 DOI: 10.1021/acs.biochem.7b00470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nod2 is a cytosolic, innate immune receptor responsible for binding to bacterial cell wall fragments such as muramyl dipeptide (MDP). Upon binding, subsequent downstream activation of the NF-κB pathway leads to an immune response. Nod2 mutations are correlated with an increased susceptibility to Crohn's disease (CD) and ultimately result in a misregulated immune response. Previous work had demonstrated that Nod2 interacts with and is stabilized by the molecular chaperone Hsp70. In this work, it is shown using purified protein and in vitro biochemical assays that the critical Nod2 CD mutations (G908R, R702W, and 1007fs) preserve the ability to bind bacterial ligands. A limited proteolysis assay and luciferase reporter assay reveal regions of Hsp70 that are capable of stabilizing Nod2 and rescuing CD mutant activity. A minimal 71-amino acid subset of Hsp70 that stabilizes the CD-associated variants of Nod2 and restores a proper immune response upon activation with MDP was identified. This work suggests that CD-associated Nod2 variants could be stabilized in vivo with a molecular chaperone.
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Affiliation(s)
- Amy K Schaefer
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - Hannah C Wastyk
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - Vishnu Mohanan
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - Ching-Wen Hou
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - Mackenzie L Lauro
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - James E Melnyk
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - Jason M Burch
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry and ‡Department of Biological Sciences, University of Delaware , Newark, Delaware 19716, United States
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