1
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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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2
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Polyakov VR, Alexandrov V, Maderna A, Bajjuri K, Li X, Zhou S. Indexing Ultrafast Shape-Based Descriptors in MongoDB to Identify TLR4 Pathway Agonists. J Chem Inf Model 2022; 62:2446-2455. [PMID: 35522137 DOI: 10.1021/acs.jcim.2c00156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A method is presented for an ultrafast shape-based search workflow for the screening of large compound collections, i.e., those of vendors. The three-dimensional shape of a molecule dictates its biological activity by enabling the molecule to fit into binding pockets of proteins. Quite often, distinctly different chemical compounds that have similar shapes can bind in a similar way. OpenEye pioneered an algorithm for comparing shapes of molecules by overlaying them in a computer and measuring differences between a query molecule and a target molecule. Overlaying shapes is a computationally intensive process and represents a bottleneck in searching for similar molecules. More recent publications describe alternative methods of overlaying molecules, which are accomplished by comparing shape-based descriptors. These methods were implemented in the Open Drug Discovery Toolkit (ODDT) package. We utilized a combination of open-source software packages like ODDT and RDkit to implement a workflow for ultrafast conformer generation and matching that does not require storing precomputed conformers on the file system or in memory. Moreover, the generated descriptors could be optionally stored in MongoDB for performing searches in the future. To speed up the search, we created a set of indexes from the transformed shape-based descriptors. We are in the process of calculating descriptors for multiple vendors, including Enamine's "REAL" collection of 1.2 billion compounds. Currently, the shape similarity search on more than 70 million compounds takes less than 8 s! We exemplified our methodology with the screen of compounds that can act as putative TLR4 agonists. The search was based on a literature-known small-molecule TLR4 agonist series. In due course, we identified compounds with novel structural motifs that were active in mouse and human TLR4 reporter cell lines.
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Affiliation(s)
- Valery R Polyakov
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Vadim Alexandrov
- Liquid Algo LLC, 85 Thistle Ln, Hopewell Junction, New York 12533, United States
| | - Andreas Maderna
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Krishna Bajjuri
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Xiaofan Li
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Sihong Zhou
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
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3
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Bayan N, Yazdanpanah N, Rezaei N. Role of Toll-Like Receptor 4 in Diabetic Retinopathy. Pharmacol Res 2021; 175:105960. [PMID: 34718133 DOI: 10.1016/j.phrs.2021.105960] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 12/11/2022]
Abstract
Diabetic retinopathy (DR) is the most frequent microvascular complication of diabetes mellitus (DM) and a leading cause of blindness worldwide. Evidence has shown that DR is an inflammatory disease with hyperglycemia playing a causative role in the development of its main features, including inflammation, cellular apoptosis, neurodegeneration, oxidative stress, and neovascularization. Toll-like receptors (TLRs) are a well-known family of pattern recognition receptors (PRRs) responsible for the initiation of inflammatory and immune responses. TLR4 identifies both endogenous and exogenous ligands and is associated with various physiological and pathological pathways in the body. While the detailed pathophysiology of DR is still unclear, increasing data suggests a crucial role for TLR4 in the development of DR. Due to hyperglycemia, TLR4 expression increases in diabetic retina, which activates various pathways leading to DR. Considering the role of TLR4 in DR, several studies have focused on the association of TLR4 polymorphisms and risk of DR development. Moreover, evidence concerning the effect of microRNAs in the pathogenesis of DR, through their interaction with TLR4, indicates the determinant role of TLR4 in this disease. Of note, several agents have proven as effective in alleviating DR through the inhibition of the TLR4 pathway, suggesting new avenues in DR treatment. In this review, we provided a brief overview of the TLR4 structure and biological function and a more comprehensive discussion about the mechanisms of TLR4 activation in DR. Furthermore, we summarized the relationship between TLR4 polymorphisms and risk of DR and the relationship between microRNAs and TLR4 in DR. Finally, we discussed the current progress in designing TLR4 inhibitors, which could be helpful in DR clinical management.
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Affiliation(s)
- Nikoo Bayan
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Niloufar Yazdanpanah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Nunes PSG, da Silva G, Nascimento S, Mantoani SP, de Andrade P, Bernardes ES, Kawano DF, Leopoldino AM, Carvalho I. Synthesis, biological evaluation and molecular docking studies of novel 1,2,3-triazole-quinazolines as antiproliferative agents displaying ERK inhibitory activity. Bioorg Chem 2021; 113:104982. [PMID: 34020277 DOI: 10.1016/j.bioorg.2021.104982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022]
Abstract
ERK1/2 inhibitors have attracted special attention concerning the ability of circumventing cases of innate or log-term acquired resistance to RAF and MEK kinase inhibitors. Based on the 4-aminoquinazoline pharmacophore of kinases, herein we describe the synthesis of 4-aminoquinazoline derivatives bearing a 1,2,3-triazole stable core to bridge different aromatic and heterocyclic rings using copper-catalysed azide-alkyne cycloaddition reaction (CuAAC) as a Click Chemistry strategy. The initial screening of twelve derivatives in tumoral cells (CAL-27, HN13, HGC-27, and BT-20) revealed that the most active in BT-20 cells (25a, IC50 24.6 μM and a SI of 3.25) contains a more polar side chain (sulfone). Furthermore, compound 25a promoted a significant release of lactate dehydrogenase (LDH), suggesting the induction of cell death by necrosis. In addition, this compound induced G0/G1 stalling in BT-20 cells, which was accompanied by a decrease in the S phase. Western blot analysis of the levels of p-STAT3, p-ERK, PARP, p53 and cleaved caspase-3 revealed p-ERK1/2 and p-STA3 were drastically decreased in BT-20 cells under 25a incubation, suggesting the involvement of these two kinases in the mechanisms underlying 25a-induced cell cycle arrest, besides loss of proliferation and viability of the breast cancer cell. Molecular docking simulations using the ERK-ulixertinib crystallographic complex showed compound 25a could potentially compete with ATP for binding to ERK in a slightly higher affinity than the reference ERK1/2 inhibitor. Further in silico analyses showed comparable toxicity and pharmacokinetic profiles for compound 25a in relation to ulixertinib.
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Affiliation(s)
| | - Gabriel da Silva
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Sofia Nascimento
- Radiopharmacy Center, Nuclear and Energy Research Institute (IPEN/CNEN-SP), São Paulo, São Paulo, Brazil
| | | | - Peterson de Andrade
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Emerson Soares Bernardes
- Radiopharmacy Center, Nuclear and Energy Research Institute (IPEN/CNEN-SP), São Paulo, São Paulo, Brazil
| | - Daniel Fábio Kawano
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Andreia Machado Leopoldino
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ivone Carvalho
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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5
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Abstract
Personalized cancer vaccines (PCVs) are reinvigorating vaccine strategies in cancer immunotherapy. In contrast to adoptive T-cell therapy and checkpoint blockade, the PCV strategy modulates the innate and adaptive immune systems with broader activation to redeploy antitumor immunity with individualized tumor-specific antigens (neoantigens). Following a sequential scheme of tumor biopsy, mutation analysis, and epitope prediction, the administration of neoantigens with synthetic long peptide (SLP) or mRNA formulations dramatically improves the population and activity of antigen-specific CD4+ and CD8+ T cells. Despite the promising prospect of PCVs, there is still great potential for optimizing prevaccination procedures and vaccine potency. In particular, the arduous development of tumor-associated antigen (TAA)-based vaccines provides valuable experience and rational principles for augmenting vaccine potency which is expected to advance PCV through the design of adjuvants, delivery systems, and immunosuppressive tumor microenvironment (TME) reversion since current personalized vaccination simply admixes antigens with adjuvants. Considering the broader application of TAA-based vaccine design, these two strategies complement each other and can lead to both personalized and universal therapeutic methods. Chemical strategies provide vast opportunities for (1) exploring novel adjuvants, including synthetic molecules and materials with optimizable activity, (2) constructing efficient and precise delivery systems to avoid systemic diffusion, improve biosafety, target secondary lymphoid organs, and enhance antigen presentation, and (3) combining bioengineering methods to innovate improvements in conventional vaccination, "smartly" re-educate the TME, and modulate antitumor immunity. As chemical strategies have proven versatility, reliability, and universality in the design of T cell- and B cell-based antitumor vaccines, the union of such numerous chemical methods in vaccine construction is expected to provide new vigor and vitality in cancer treatment.
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Affiliation(s)
- Wen-Hao Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, 100084 Beijing, China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, 100084 Beijing, China.,Beijing Institute for Brain Disorders, 100069 Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, 100084 Beijing, China
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6
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Zlotin SG, Dalinger IL, Makhova NN, Tartakovsky VA. Nitro compounds as the core structures of promising energetic materials and versatile reagents for organic synthesis. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4908] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review addresses some promising areas of chemistry of nitro compounds extensively developed in recent years in Russia (particularly at the N.D.Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences) and worldwide. The most important results in the synthesis of novel energetic N-, C- and O-nitro compounds are summarized. New environmentally friendly approaches to the preparation of known compounds of this series, used as components of energetic compositions, are considered. Methods for selective transformations of various nitro compounds to valuable products of organic synthesis, primarily biologically active products and their precursors, are systematically analyzed.
The bibliography includes 446 references.
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7
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Recent advancements of 4-aminoquinazoline derivatives as kinase inhibitors and their applications in medicinal chemistry. Eur J Med Chem 2019; 170:55-72. [DOI: 10.1016/j.ejmech.2019.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/21/2019] [Accepted: 03/01/2019] [Indexed: 12/30/2022]
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8
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Ignacio BJ, Albin TJ, Esser-Kahn AP, Verdoes M. Toll-like Receptor Agonist Conjugation: A Chemical Perspective. Bioconjug Chem 2018; 29:587-603. [PMID: 29378134 PMCID: PMC10642707 DOI: 10.1021/acs.bioconjchem.7b00808] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Toll-like receptors (TLRs) are vital elements of the mammalian immune system that function by recognizing pathogen-associated molecular patterns (PAMPs), bridging innate and adaptive immunity. They have become a prominent therapeutic target for the treatment of infectious diseases, cancer, and allergies, with many TLR agonists currently in clinical trials or approved as immunostimulants. Numerous studies have shown that conjugation of TLR agonists to other molecules can beneficially influence their potency, toxicity, pharmacokinetics, or function. The functional properties of TLR agonist conjugates, however, are highly dependent on the ligation strategy employed. Here, we review the chemical structural requirements for effective functional TLR agonist conjugation. In addition, we provide similar analysis for those that have yet to be conjugated. Moreover, we discuss applications of covalent TLR agonist conjugation and their implications for clinical use.
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Affiliation(s)
- Bob J. Ignacio
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tyler J. Albin
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Aaron P. Esser-Kahn
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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9
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Honegr J, Malinak D, Dolezal R, Soukup O, Benkova M, Hroch L, Benek O, Janockova J, Kuca K, Prymula R. Rational design of novel TLR4 ligands by in silico screening and their functional and structural characterization in vitro. Eur J Med Chem 2018; 146:38-46. [PMID: 29407964 DOI: 10.1016/j.ejmech.2017.12.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022]
Abstract
The purpose of this study was to identify new small molecules that possess activity on human toll-like receptor 4 associated with the myeloid differentiation protein 2 (hTLR4/MD2). Following current rational drug design principles, we firstly performed a ligand and structure based virtual screening of more than 130 000 compounds to discover until now unknown class of hTLR4/MD2 modulators that could be used as novel type of immunologic adjuvants. The core of the in silico study was molecular docking of flexible ligands in a partially flexible hTLR4/MD2 receptor model using a peta-flops-scale supercomputer. The most promising substances resulting from this study, related to anthracene-succimide hybrids, were synthesized and tested. The best prepared candidate exhibited 80% of Monophosphoryl Lipid A in vitro agonistic activity in cell lines expressing hTLR4/MD2.
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Affiliation(s)
- Jan Honegr
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; Department of Intensive Medicine and Forensic Science, Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
| | - David Malinak
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Rafael Dolezal
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Marketa Benkova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Lukas Hroch
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Ondrej Benek
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Jana Janockova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Roman Prymula
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
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Martinez-Gil L, Goff PH, Tan GS. The Role of Self-Assembling Lipid Molecules in Vaccination. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2018. [PMCID: PMC7147077 DOI: 10.1016/bs.abl.2017.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The advent of vaccines represents one of the most significant advances in medical history. The protection provided by vaccines has greatly contributed in reducing the number of cases of infections and most notably to the eradication of small pox. A large number of new technologies and approaches in vaccine development are currently being investigated with the goal of providing the basis for the next generation of prophylactics against an ever-expanding list of emerging and reemerging pathogens. In this chapter, we will focus on the role of lipids and lipid self-assembling vesicles in new and promising vaccination approaches. We will start by describing how lipids can induce activation of the innate immune system and focus on some lipid-derived vaccine adjuvants. Next, we will review current lipid-based self-assembling particles used as vaccine platforms, specifically liposomes and virus-like particles, and how virus-like particles have facilitated research of highly pathogenic viruses such as Ebola.
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11
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Cochet F, Peri F. The Role of Carbohydrates in the Lipopolysaccharide (LPS)/Toll-Like Receptor 4 (TLR4) Signalling. Int J Mol Sci 2017; 18:E2318. [PMID: 29099761 PMCID: PMC5713287 DOI: 10.3390/ijms18112318] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/27/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022] Open
Abstract
The interactions between sugar-containing molecules from the bacteria cell wall and pattern recognition receptors (PRR) on the plasma membrane or cytosol of specialized host cells are the first molecular events required for the activation of higher animal's immune response and inflammation. This review focuses on the role of carbohydrates of bacterial endotoxin (lipopolysaccharide, LPS, lipooligosaccharide, LOS, and lipid A), in the interaction with the host Toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD-2) complex. The lipid chains and the phosphorylated disaccharide core of lipid A moiety are responsible for the TLR4 agonist action of LPS, and the specific interaction between MD-2, TLR4, and lipid A are key to the formation of the activated complex (TLR4/MD-2/LPS)₂, which starts intracellular signalling leading to nuclear factors activation and to production of inflammatory cytokines. Subtle chemical variations in the lipid and sugar parts of lipid A cause dramatic changes in endotoxin activity and are also responsible for the switch from TLR4 agonism to antagonism. While the lipid A pharmacophore has been studied in detail and its structure-activity relationship is known, the contribution of core saccharides 3-deoxy-d-manno-octulosonic acid (Kdo) and heptosyl-2-keto-3-deoxy-octulosonate (Hep) to TLR4/MD-2 binding and activation by LPS and LOS has been investigated less extensively. This review focuses on the role of lipid A, but also of Kdo and Hep sugars in LPS/TLR4 signalling.
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Affiliation(s)
- Florent Cochet
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy.
| | - Francesco Peri
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy.
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Chan M, Kakitsubata Y, Hayashi T, Ahmadi A, Yao S, Shukla NM, Oyama SY, Baba A, Nguyen B, Corr M, Suda Y, Carson DA, Cottam HB, Wakao M. Structure-Activity Relationship Studies of Pyrimido[5,4-b]indoles as Selective Toll-Like Receptor 4 Ligands. J Med Chem 2017; 60:9142-9161. [PMID: 29049886 DOI: 10.1021/acs.jmedchem.7b00797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Previous high throughput screening studies led to the discovery of two novel, nonlipid-like chemotypes as Toll-like receptor 4 (TLR4) agonists. One of these chemotypes, the pyrimido[5,4-b]indoles, was explored for structure-activity relationship trends relative to production of TLR4 dependent cytokines/chemokines, resulting in a semioptimized lead (compound 1) that provided a starting point for further optimization studies. In this report, compounds belonging to three areas of structural modification were evaluated for biological activity using murine and human TLR4 reporter cells, primary murine bone marrow derived dendritic cells, and human peripheral blood mononuclear cells. The compounds bearing certain aryl groups at the C8 position, such as phenyl (36) and β-naphthyl (39), had potencies significantly greater than compound 1. Compound 36 displayed human TLR4 agonist activity at submicromolar concentrations. The computational analysis suggests that the improved potency of these C8-aryl derivatives may be the result of additional binding interactions at the interface of the TLR4/myeloid differentiation protein-2 (MD-2) complex.
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Affiliation(s)
- Michael Chan
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Yuhei Kakitsubata
- Department of Chemistry, Kagoshima University , 1-21-40 Kohrimoto, 890-0065, Kagoshima, Japan
| | - Tomoko Hayashi
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Alast Ahmadi
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Shiyin Yao
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Nikunj M Shukla
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Shin-Ya Oyama
- Department of Chemistry, Kagoshima University , 1-21-40 Kohrimoto, 890-0065, Kagoshima, Japan
| | - Akihito Baba
- Department of Chemistry, Kagoshima University , 1-21-40 Kohrimoto, 890-0065, Kagoshima, Japan
| | - Brandon Nguyen
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Maripat Corr
- Department of Medicine, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Yasuo Suda
- Department of Chemistry, Kagoshima University , 1-21-40 Kohrimoto, 890-0065, Kagoshima, Japan
| | - Dennis A Carson
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States.,Department of Medicine, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Howard B Cottam
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States.,Department of Medicine, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0695, United States
| | - Masahiro Wakao
- Moores Cancer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0695, United States.,Department of Chemistry, Kagoshima University , 1-21-40 Kohrimoto, 890-0065, Kagoshima, Japan
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13
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Chan M, Ahmadi A, Yao S, Sato-Kaneko F, Messer K, Pu M, Nguyen B, Hayashi T, Corr M, Carson DA, Cottam HB, Shukla NM. Identification of Biologically Active Pyrimido[5,4-b]indoles That Prolong NF-κB Activation without Intrinsic Activity. ACS COMBINATORIAL SCIENCE 2017; 19:533-543. [PMID: 28657707 DOI: 10.1021/acscombsci.7b00080] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Most vaccine adjuvants directly stimulate and activate antigen presenting cells but do not sustain immunostimulation of these cells. A high throughput screening (HTS) strategy was designed to identify compounds that would sustain NF-κB activation by a stimulus from the Toll-like receptor (TLR)4 ligand, lipopolysaccharide (LPS). Several pilot studies optimized the parameters and conditions for a cell based NF-κB reporter assay in human monocytic THP-1 cells. The final assay evaluated prolongation of LPS induced NF-κB activation at 12 h. The dynamic range of the assay was confirmed in a pilot screen of 14 631 compounds and subsequently in a main extensive screen with 166 304 compounds. Hit compounds were identified using an enrichment strategy based on unsupervised chemoinformatic clustering, and also by a naı̈ve "Top X" approach. A total of 2011 compounds were then rescreened for levels of coactivation with LPS at 5 h and 12 h, which provided kinetic profiles. Of the 407 confirmed hits, compounds that showed correlation of the kinetic profiles with the structural similarities led to identification of four chemotypes: pyrimido[5,4-b]indoles, 4H-chromene-3-carbonitriles, benzo[d][1,3]dioxol-2-ylureas, and tetrahydrothieno[2,3-c]pyridines, which were segregated by 5 h and 12 h kinetic characteristics. Unlike the TLR4 agonistic pyrimidoindoles identified in previous studies, the revealed pyrimidoindoles in the present work did not intrinsically stimulate TLR4 nor induce NF-κB but rather prolonged NF-κB signaling induced by LPS. A 42-member combinatorial library was synthesized which led to identification of potent N3-alkyl substituted pyrimidoindoles that were not only active in vitro but also enhanced antibody responses in vivo when used as a coadjuvant. The novel HTS strategy led to identification of compounds that are intrinsically quiescent but functionally prolong stimulation by a TLR4 ligand and thereby potentiate vaccine efficacy.
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Affiliation(s)
- Michael Chan
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Alast Ahmadi
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Shiyin Yao
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Fumi Sato-Kaneko
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Karen Messer
- Division
of Biostatistics, University of California San Diego, La Jolla, California 92093, United States
| | - Minya Pu
- Division
of Biostatistics, University of California San Diego, La Jolla, California 92093, United States
| | - Brandon Nguyen
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Tomoko Hayashi
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Maripat Corr
- Department
of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Dennis A. Carson
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Howard B. Cottam
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Nikunj M. Shukla
- Moores
UCSD Cancer Center, University of California San Diego, La Jolla, California 92093, United States
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14
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Marshall JD, Heeke DS, Rao E, Maynard SK, Hornigold D, McCrae C, Fraser N, Tovchigrechko A, Yu L, Williams N, King S, Cooper ME, Hajjar AM, Woo JC. A Novel Class of Small Molecule Agonists with Preference for Human over Mouse TLR4 Activation. PLoS One 2016; 11:e0164632. [PMID: 27736941 PMCID: PMC5063506 DOI: 10.1371/journal.pone.0164632] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/28/2016] [Indexed: 01/09/2023] Open
Abstract
The best-characterized Toll-like receptor 4 (TLR4) ligands are lipopolysaccharide (LPS) and its chemically modified and detoxified variant, monophosphoryl lipid A (MPL). Although both molecules are active for human TLR4, they demonstrate a potency preference for mouse TLR4 based on data from transfected cell lines and primary cells of both species. After a high throughput screening process of small molecule libraries, we have discovered a new class of TLR4 agonist with a species preference profile differing from MPL. Products of the 4-component Ugi synthesis reaction were demonstrated to potently trigger human TLR4-transfected HEK cells but not mouse TLR4, although inclusion of the human MD2 with mTLR4 was able to partially recover activity. Co-expression of CD14 was not required for optimal activity of Ugi compounds on transfected cells, as it is for LPS. The species preference profile for the panel of Ugi compounds was found to be strongly active for human and cynomolgus monkey primary cells, with reduced but still substantial activity for most Ugi compounds on guinea pig cells. Mouse, rat, rabbit, ferret, and cotton rat cells displayed little or no activity when exposed to Ugi compounds. However, engineering the human versions of TLR4 and MD2 to be expressed in mTLR4/MD2 deficient mice allowed for robust activity by Ugi compounds both in vitro and in vivo. These findings extend the range of compounds available for development as agonists of TLR4 and identify novel molecules which reverse the TLR4 triggering preference of MPL for mouse TLR4 over human TLR4. Such compounds may be amenable to formulation as more potent human-specific TLR4L-based adjuvants than typical MPL-based adjuvants.
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Affiliation(s)
- Jason D. Marshall
- Vaccine Platform Group, MedImmune, Gaithersburg, Maryland, United States of America
- * E-mail:
| | - Darren S. Heeke
- Translational Biology Group, MedImmune, Mountain View, California, United States of America
| | - Eileen Rao
- Translational Biology Group, MedImmune, Mountain View, California, United States of America
| | - Sean K. Maynard
- Vaccine Platform Group, MedImmune, Gaithersburg, Maryland, United States of America
| | - David Hornigold
- Department of Cardiovascular and Metabolic Diseases, MedImmune, Cambridge, United Kingdom
| | - Christopher McCrae
- Translational Science, Respiratory, Inflammation and Autoimmunity Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Neil Fraser
- Biology Department, AstraZeneca R&D, Charnwood, United Kingdom
| | - Andrey Tovchigrechko
- Research Bioinformatics, MedImmune, Gaithersburg, Maryland, United States of America
| | - Li Yu
- Statistical Sciences, MedImmune, Gaithersburg, Maryland, United States of America
| | - Nicola Williams
- Biology Department, AstraZeneca R&D, Charnwood, United Kingdom
| | - Sarah King
- Medicinal Chemistry Department, AstraZeneca R&D, Charnwood, United Kingdom
| | - Martin E. Cooper
- Translational Science, Respiratory, Inflammation and Autoimmunity Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Adeline M. Hajjar
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jennifer C. Woo
- Translational Biology Group, MedImmune, Mountain View, California, United States of America
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15
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Billod JM, Lacetera A, Guzmán-Caldentey J, Martín-Santamaría S. Computational Approaches to Toll-Like Receptor 4 Modulation. Molecules 2016; 21:molecules21080994. [PMID: 27483231 PMCID: PMC6274477 DOI: 10.3390/molecules21080994] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 01/07/2023] Open
Abstract
Toll-like receptor 4 (TLR4), along with its accessory protein myeloid differentiation factor 2 (MD-2), builds a heterodimeric complex that specifically recognizes lipopolysaccharides (LPS), which are present on the cell wall of Gram-negative bacteria, activating the innate immune response. Some TLR4 modulators are undergoing preclinical and clinical evaluation for the treatment of sepsis, inflammatory diseases, cancer and rheumatoid arthritis. Since the relatively recent elucidation of the X-ray crystallographic structure of the extracellular domain of TLR4, research around this fascinating receptor has risen to a new level, and thus, new perspectives have been opened. In particular, diverse computational techniques have been applied to decipher some of the basis at the atomic level regarding the mechanism of functioning and the ligand recognition processes involving the TLR4/MD-2 system at the atomic level. This review summarizes the reported molecular modeling and computational studies that have recently provided insights into the mechanism regulating the activation/inactivation of the TLR4/MD-2 system receptor and the key interactions modulating the molecular recognition process by agonist and antagonist ligands. These studies have contributed to the design and the discovery of novel small molecules with promising activity as TLR4 modulators.
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Affiliation(s)
| | | | - Joan Guzmán-Caldentey
- Department of Chemical & Physical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, C/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Sonsoles Martín-Santamaría
- Department of Chemical & Physical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, C/Ramiro de Maeztu 9, 28040 Madrid, Spain.
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16
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Wu TYH. Strategies for designing synthetic immune agonists. Immunology 2016; 148:315-25. [PMID: 27213842 DOI: 10.1111/imm.12622] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/04/2016] [Accepted: 05/18/2016] [Indexed: 12/16/2022] Open
Abstract
Enhancing the immune system is a validated strategy to combat infectious disease, cancer and allergy. Nevertheless, the development of immune adjuvants has been hampered by safety concerns. Agents that can stimulate the immune system often bear structural similarities with pathogen-associated molecular patterns found in bacteria or viruses and are recognized by pattern recognition receptors (PRRs). Activation of these PRRs results in the immediate release of inflammatory cytokines, up-regulation of co-stimulatory molecules, and recruitment of innate immune cells. The distribution and duration of these early inflammatory events are crucial in the development of antigen-specific adaptive immunity in the forms of antibody and/or T cells capable of searching for and destroying the infectious pathogens or cancer cells. However, systemic activation of these PRRs is often poorly tolerated. Hence, different strategies have been employed to modify or deliver immune agonists in an attempt to control the early innate receptor activation through temporal or spatial restriction. These approaches include physicochemical manipulation, covalent conjugation, formulation and conditional activation/deactivation. This review will describe recent examples of discovery and optimization of synthetic immune agonists towards clinical application.
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17
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Salyer ACD, Caruso G, Khetani KK, Fox LM, Malladi SS, David SA. Identification of Adjuvantic Activity of Amphotericin B in a Novel, Multiplexed, Poly-TLR/NLR High-Throughput Screen. PLoS One 2016; 11:e0149848. [PMID: 26919709 PMCID: PMC4769227 DOI: 10.1371/journal.pone.0149848] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/05/2016] [Indexed: 01/26/2023] Open
Abstract
Small-molecule agonists have been identified for TLR7, TLR8, TLR4 and TLR2 thus far, and chemotypes other than those of canonical ligands are yet to be explored for a number of innate immune receptors. The discovery of novel immunostimulatory molecules would enhance the repertoire of tools available for interrogating innate immune effector mechanisms, and provide additional venues for vaccine adjuvant development. A multiplexed, reporter gene-based high-throughput assay capable of detecting agonists of TLR2, TLR3, TLR4, TLR5, TLR7, TLR8, TLR9, NOD1 and NOD2 was utilized in screening 123,943 compounds, in which amphotericin B (AmpB) and nystatin were identified as prominent hits. The polyene antifungal agents act as TLR2- and TLR4-agonists. The TLR4-stimulatory activity of AmpB was similar to that of monophosphoryl lipid A, suggestive of TRIF-biased signaling. The adjuvantic activity of AmpB, at a dose of 100 micrograms, was comparable to several other candidate adjuvants in rabbit models of immunization. These results point to its potential applicability as a safe and effective adjuvant for human vaccines.
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Affiliation(s)
- Alex C. D. Salyer
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas, United States of America
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Giuseppe Caruso
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Karishma K. Khetani
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Lauren M. Fox
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Subbalakshmi S. Malladi
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Sunil A. David
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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18
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Stutts L, Esser-Kahn AP. A Light-Controlled TLR4 Agonist and Selectable Activation of Cell Subpopulations. Chembiochem 2015; 16:1744-8. [PMID: 26097006 PMCID: PMC4881745 DOI: 10.1002/cbic.201500164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 11/07/2022]
Abstract
The spatial and temporal aspects of immune cell signaling are key parameters in defining the magnitude of an immune response. Toll-like receptors (TLRs) on innate immune cells are important in the early detection of pathogens and initiation of an immune response. Controlling the spatial and temporal signaling of TLRs would enable further study of immune synergies and assist in the development of new vaccines. Here, we show a light-based method for the spatial control of TLR4 signaling. A TLR4 agonist, pyrimido[5,4-b]indole, was protected with a cage at a position critical for receptor binding. This afforded a photocontrollable agonist that was inactive while caged, yet effected NF-κB activity in cells following UV photocontrolled deprotection. We demonstrated spatial control of NF-κB activation within a population of cells by treating all cells with the caged TLR4 agonist and constraining light exposure and consequent activation to a region of interest.
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Affiliation(s)
- Lalisa Stutts
- Department of Chemistry, University of California, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Aaron P Esser-Kahn
- Department of Chemistry, University of California, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA).
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