1
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Shukla NM, Sato-Kaneko F, Yao S, Pu M, Chan M, Lao FS, Sako Y, Saito T, Messer K, Hayashi T, Cottam HB, Corr M, Carson DA. A Triple High Throughput Screening for Extracellular Vesicle Inducing Agents With Immunostimulatory Activity. Front Pharmacol 2022; 13:869649. [PMID: 35479316 PMCID: PMC9035538 DOI: 10.3389/fphar.2022.869649] [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: 02/04/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular vesicles (EVs) play an important role in intercellular communication and regulation of cells, especially in the immune system where EVs can participate in antigen presentation and may have adjuvant effects. We aimed to identify small molecule compounds that can increase EV release and thereby enhance the immunogenicity of vaccines. We utilized a THP-1 reporter cell line engineered to release EV-associated tetraspanin (CD63)-Turbo-luciferase to quantitatively measure EVs released in culture supernatants as a readout of a high throughput screen (HTS) of 27,895 compounds. In parallel, the cytotoxicity of the compounds was evaluated by PrestoBlue dye assay. For screening immunostimulatory potency, we performed two additional independent HTS on the same compound library using NF-κB and interferon-stimulated response element THP-1 reporter cell lines. Hit compounds were then identified in each of the 3 HTS’s, using a “Top X″ and a Gaussian Mixture Model approach to rule out false positive compounds and to increase the sensitivity of the hit selection. Thus, 644 compounds were selected as hits which were further evaluated for induction of IL-12 in murine bone-marrow derived dendritic cells (mBMDCs) and for effects of cell viability. The resulting 130 hits were then assessed from a medicinal chemistry perspective to remove compounds with functional group liabilities. Finally, 80 compounds were evaluated as vaccine adjuvants in vivo using ovalbumin as a model antigen. We analyzed 18 compounds with adjuvant activity for their ability to induce the expression of co-stimulatory molecules on mBMDCs. The full complement of data was then used to cluster the compounds into 4 distinct biological activity profiles. These compounds were also evaluated for quantitation of EV release and spider plot overlays were generated to compare the activity profiles of compounds within each cluster. This tiered screening process identified two compounds that belong to the 4-thieno-2-thiopyrimidine scaffold with identical screening profiles supporting data reproducibility and validating the overall screening process. Correlation patterns in the adjuvanticity data suggested a role for CD63 and NF-κB pathways in potentiating antigen-specific antibody production. Thus, our three independent cell-based HTS campaigns led to identification of immunostimulatory compounds that release EVs and have adjuvant activity.
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Affiliation(s)
- Nikunj M. Shukla
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Fumi Sato-Kaneko
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Shiyin Yao
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Minya Pu
- The Herbert Wertheim School of Public Health and Longevity, University of California San Diego, La Jolla, CA, United States
| | - Michael Chan
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Fitzgerald S. Lao
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Yukiya Sako
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Tetsuya Saito
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Karen Messer
- The Herbert Wertheim School of Public Health and Longevity, University of California San Diego, La Jolla, CA, United States
| | - Tomoko Hayashi
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Howard B. Cottam
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Maripat Corr
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Dennis A. Carson
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
- *Correspondence: Dennis A. Carson,
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2
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Saito T, Shukla NM, Sato-Kaneko F, Sako Y, Hosoya T, Yao S, Lao FS, Messer K, Pu M, Chan M, Chu PJ, Cottam HB, Hayashi T, Carson DA, Corr M. Small Molecule Calcium Channel Activator Potentiates Adjuvant Activity. ACS Chem Biol 2022; 17:217-229. [PMID: 34985883 PMCID: PMC8788586 DOI: 10.1021/acschembio.1c00883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/21/2021] [Indexed: 01/07/2023]
Abstract
There remains an unmet need for reliable fully synthetic adjuvants that increase lasting protective immune responses from vaccines. We previously reported a high-throughput screening for small molecules that extended nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB) activation after a Toll-like receptor 4 (TLR4) ligand, lipopolysaccharide (LPS), stimulation using a human myeloid reporter cell line. We identified compounds with a conserved aminothiazole scaffold including 2D216 [N-(4-(2,5-dimethylphenyl)thiazol-2-yl)-4-(piperidin-1-ylsulfonyl)benzamide], which increased murine antigen-specific antibody responses when used as a co-adjuvant with LPS. Here, we examined the mechanism of action in human cells. Although 2D216 activated the major mitogen-activated protein kinases, it did not interact with common kinases and phosphatases and did not stimulate many of the pattern recognition receptors (PRRs). Instead, the mechanism of action was linked to intracellular Ca2+ elevation via Ca2+ channel(s) at the plasma membrane and nuclear translocation of the nuclear factor of activated T-cells (NFAT) as supported by RNA-seq data, analysis by reporter cells, Ca2+ flux assays, and immunoblots. Interestingly, 2D216 had minimal, if any, activity on Jurkat T cells but induced cytokine production and surface expression of costimulatory molecules on cells with antigen-presenting functions. A small series of analogs of 2D216 were tested for the ability to enhance a TLR4 ligand-stimulated autologous mixed lymphocyte reaction (MLR). In the MLR, 2E151, N-(4-(2,5-dimethylphenyl)thiazol-2-yl)-4-((4-propylpiperidin-1-yl)sulfonyl)benzamide, was more potent than 2D216. These results indicate that a small molecule that is not a direct PRR agonist can act as a co-adjuvant to an approved adjuvant to enhance human immune responses via a complementary mechanism of action.
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Affiliation(s)
- Tetsuya Saito
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
- Department
of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Nikunj M. Shukla
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Fumi Sato-Kaneko
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Yukiya Sako
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Tadashi Hosoya
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
- Department
of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Shiyin Yao
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Fitzgerald S. Lao
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Karen Messer
- Herbert
Wertheim School of Public Health and Longevity, University of California San Diego, La Jolla, California 92093-0901, United States
| | - Minya Pu
- Herbert
Wertheim School of Public Health and Longevity, University of California San Diego, La Jolla, California 92093-0901, United States
| | - Michael Chan
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Paul J. Chu
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Howard B. Cottam
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Tomoko Hayashi
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Dennis A. Carson
- Moores
Cancer Center, University of California
San Diego, La Jolla, California 92093-0809, United States
| | - Maripat Corr
- Department
of Medicine, University of California San
Diego, La Jolla, California 92093-0656, United States
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3
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Hosoya T, Shukla NM, Fujita Y, Yao S, Lao FS, Baba H, Yasuda S, Cottam HB, Carson DA, Hayashi T, Corr M. Identification of Compounds With Glucocorticoid Sparing Effects on Suppression of Chemokine and Cytokine Production by Rheumatoid Arthritis Fibroblast-Like Synoviocytes. Front Pharmacol 2020; 11:607713. [PMID: 33390996 PMCID: PMC7773657 DOI: 10.3389/fphar.2020.607713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years target based drug discovery has expanded our therapeutic armamentarium in the treatment of inflammatory and autoimmune diseases. Despite these advances and adverse effects, glucocorticoids remain reliable agents that are used in many of these diseases. The anti-inflammatory mechanisms of glucocorticoids include the suppression of transcription factor activity like nuclear factor kappa B (NF-κB). By reanalyzing data from two prior high throughput screens (HTS) that utilized a NF-κB reporter construct in THP-1 cells, we identified 1824 small molecule synthetic compounds that demonstrated NF-κB suppressive activities similar to the glucocorticoids included in the original >134,000 compound libraries. These 1824 compounds were then rescreened for attenuating NF-κB activity at 5 and 16 h after LPS stimuli in the NF-κB THP-1 reporter cells. After a “Top X” selection approach 122 hit compounds were further tested for toxicity and suppression of LPS induced CXCL8 release in THP-1 cells. Excluding cytotoxic compounds, the remaining active compounds were grouped into chemotype families using Tanimoto based clustering. Promising representatives from clustered chemotype groups were commercially purchased for further testing. Amongst these index compounds a lead chemotype: 1H-pyrazolo [3,4 d] pyrimidin-4-amine, effectively suppressed CXCL8, and TNF production by THP-1 cells when stimulated with LPS, TNF or IL-1ß. Extending these studies to primary cells, these lead compounds also reduced IL-6 and CXCL8 production by TNF stimulated fibroblast-like synoviocytes (FLS) from rheumatoid arthritis (RA) patients. Importantly a lead 1H-pyrazolo [3,4 d] pyrimidin-4-amine compound demonstrated synergistic effects with dexamethasone when co-administered to TNF stimulated THP-1 cells and RA FLS in suppressing chemokine production. In summary, a cell based HTS approach identified lead compounds that reduced NF-κB activity and chemokine secretion induced by potent immunologic stimuli, and one lead compound that acted synergistically with dexamethasone as an anti-inflammatory agent showing a dose-sparing effect.
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Affiliation(s)
- Tadashi Hosoya
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States.,Department of Rheumatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nikunj M Shukla
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Yuya Fujita
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Shiyin Yao
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Fitzgerald S Lao
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Hiroyuki Baba
- Department of Rheumatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shinsuke Yasuda
- Department of Rheumatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Howard B Cottam
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Dennis A Carson
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Tomoko Hayashi
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Maripat Corr
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
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4
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Marchand JR, Knehans T, Caflisch A, Vitalis A. An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. J Chem Inf Model 2020; 60:5188-5202. [PMID: 32897071 DOI: 10.1021/acs.jcim.0c00558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The core task in computational drug discovery is to accurately predict binding free energies in receptor-ligand systems for large libraries of putative binders. Here, the ABSINTH implicit solvent model and force field are extended to describe small, organic molecules and their interactions with proteins. We show that an automatic pipeline based on partitioning arbitrary molecules into substructures corresponding to model compounds with known free energies of solvation can be combined with the CHARMM general force field into a method that is successful at the two important challenges a scoring function faces in virtual screening work flows: it ranks known binders with correlation values rivaling that of comparable state-of-the-art methods and it enriches true binders in a set of decoys. Our protocol introduces innovative modifications to common virtual screening workflows, notably the use of explicit ions as competitors and the integration over multiple protein and ligand species differing in their protonation states. We demonstrate the value of modifications to both the protocol and ABSINTH itself. We conclude by discussing the limitations of high-throughput implicit methods such as the one proposed here.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich, CH 8057 Zürich, Switzerland
| | - Tim Knehans
- Department of Biochemistry, University of Zürich, CH 8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH 8057 Zürich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zürich, CH 8057 Zürich, Switzerland
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5
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Bandyopadhyay D, Kreatsoulas C, Brady PG, Boyer J, He Z, Scavello G, Peryea T, Jadhav A, Nguyen DT, Guha R. Scaffold-Based Analytics: Enabling Hit-to-Lead Decisions by Visualizing Chemical Series Linked across Large Datasets. J Chem Inf Model 2019; 59:4880-4892. [DOI: 10.1021/acs.jcim.9b00243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Deepak Bandyopadhyay
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | | | - Pat G. Brady
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Joseph Boyer
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Zangdong He
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Genaro Scavello
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Tyler Peryea
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rajarshi Guha
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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6
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Shukla NM, Arimoto KI, Yao S, Fan JB, Zhang Y, Sato-Kaneko F, Lao FS, Hosoya T, Messer K, Pu M, Cottam HB, Carson DA, Hayashi T, Zhang DE, Corr M. Identification of Compounds That Prolong Type I Interferon Signaling as Potential Vaccine Adjuvants. SLAS DISCOVERY 2018; 23:960-973. [PMID: 29751735 DOI: 10.1177/2472555218774308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vaccines are reliant on adjuvants to enhance the immune stimulus, and type I interferons (IFNs) have been shown to be beneficial in augmenting this response. We were interested in identifying compounds that would sustain activation of an endogenous type I IFN response as a co-adjuvant. We began with generation of a human monocytic THP-1 cell line with an IFN-stimulated response element (ISRE)-β-lactamase reporter construct for high-throughput screening. Pilot studies were performed to optimize the parameters and conditions for this cell-based Förster resonance energy transfer (FRET) reporter assay for sustaining an IFN-α-induced ISRE activation signal. These conditions were confirmed in an initial pilot screen, followed by the main screen for evaluating prolongation of an IFN-α-induced ISRE activation signal at 16 h. Hit compounds were identified using a structure enrichment strategy based on chemoinformatic clustering and a naïve "Top X" approach. A select list of confirmed hits was then evaluated for toxicity and the ability to sustain IFN activity by gene and protein expression. Finally, for proof of concept, a panel of compounds was used to immunize mice as co-adjuvant with a model antigen and an IFN-inducing Toll-like receptor 4 agonist, lipopolysaccharide, as an adjuvant. Selected compounds significantly augmented antigen-specific immunoglobulin responses.
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Affiliation(s)
- Nikunj M Shukla
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Kei-Ichiro Arimoto
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Shiyin Yao
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jun-Bao Fan
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Yue Zhang
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Fumi Sato-Kaneko
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Fitzgerald S Lao
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tadashi Hosoya
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Karen Messer
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA.,2 Department of Family Medicine and Public Health, Division of Biostatistics and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Minya Pu
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA.,2 Department of Family Medicine and Public Health, Division of Biostatistics and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Howard B Cottam
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Dennis A Carson
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Dong-Er Zhang
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA.,3 Department of Pathology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Maripat Corr
- 4 Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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7
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Early Probe and Drug Discovery in Academia: A Minireview. High Throughput 2018; 7:ht7010004. [PMID: 29485615 PMCID: PMC5876530 DOI: 10.3390/ht7010004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 12/21/2022] Open
Abstract
Drug discovery encompasses processes ranging from target selection and validation to the selection of a development candidate. While comprehensive drug discovery work flows are implemented predominantly in the big pharma domain, early discovery focus in academia serves to identify probe molecules that can serve as tools to study targets or pathways. Despite differences in the ultimate goals of the private and academic sectors, the same basic principles define the best practices in early discovery research. A successful early discovery program is built on strong target definition and validation using a diverse set of biochemical and cell-based assays with functional relevance to the biological system being studied. The chemicals identified as hits undergo extensive scaffold optimization and are characterized for their target specificity and off-target effects in in vitro and in animal models. While the active compounds from screening campaigns pass through highly stringent chemical and Absorption, Distribution, Metabolism, and Excretion (ADME) filters for lead identification, the probe discovery involves limited medicinal chemistry optimization. The goal of probe discovery is identification of a compound with sub-µM activity and reasonable selectivity in the context of the target being studied. The compounds identified from probe discovery can also serve as starting scaffolds for lead optimization studies.
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8
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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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9
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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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10
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Synthetic Toll-like receptor 4 (TLR4) and TLR7 ligands as influenza virus vaccine adjuvants induce rapid, sustained, and broadly protective responses. J Virol 2015; 89:3221-35. [PMID: 25568203 DOI: 10.1128/jvi.03337-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Current vaccines against influenza virus infection rely on the induction of neutralizing antibodies targeting the globular head of the viral hemagglutinin (HA). Protection against seasonal antigenic drift or sporadic pandemic outbreaks requires further vaccine development to induce cross-protective humoral responses, potentially to the more conserved HA stalk region. Here, we present a novel viral vaccine adjuvant comprised of two synthetic ligands for Toll-like receptor 4 (TLR4) and TLR7. 1Z105 is a substituted pyrimido[5,4-b]indole specific for the TLR4-MD2 complex, and 1V270 is a phospholipid-conjugated TLR7 agonist. Separately, 1Z105 induces rapid Th2-associated IgG1 responses, and 1V270 potently generates Th1 cellular immunity. 1Z105 and 1V270 in combination with recombinant HA from the A/Puerto Rico/8/1934 strain (rPR/8 HA) effectively induces rapid and sustained humoral immunity that is protective against lethal challenge with a homologous virus. More importantly, immunization with the combined adjuvant and rPR/8 HA, a commercially available split vaccine, or chimeric rHA antigens significantly improves protection against both heterologous and heterosubtypic challenge viruses. Heterosubtypic protection is associated with broadly reactive antibodies to HA stalk epitopes. Histological examination and cytokine profiling reveal that intramuscular (i.m.) administration of 1Z105 and 1V270 is less reactogenic than a squalene-based adjuvant, AddaVax. In summary, the combination of 1Z105 and 1V270 with a recombinant HA induces rapid, long-lasting, and balanced Th1- and Th2-type immunity; demonstrates efficacy in a variety of murine influenza virus vaccine models assaying homologous, heterologous, and heterosubtypic challenge viruses; and has an excellent safety profile. IMPORTANCE Novel adjuvants are needed to enhance immunogenicity and increase the protective breadth of influenza virus vaccines to reduce the seasonal disease burden and ensure pandemic preparedness. We show here that the combination of synthetic Toll-like receptor 4 (TLR4) and TLR7 ligands is a potent adjuvant for recombinant influenza virus hemagglutinin, inducing rapid and sustained immunity that is protective against influenza viruses in homologous, heterologous, and heterosubtypic challenge models. Combining TLR4 and TLR7 ligands balances Th1- and Th2-type immune responses for long-lived cellular and neutralizing humoral immunity against the viral hemagglutinin. The combined adjuvant has an attractive safety profile and the potential to augment seasonal-vaccine breadth, contribute to a broadly neutralizing universal vaccine formulation, and improve response time in an emerging pandemic.
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11
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Skuta C, Bartůněk P, Svozil D. InCHlib - interactive cluster heatmap for web applications. J Cheminform 2014; 6:44. [PMID: 25264459 PMCID: PMC4173117 DOI: 10.1186/s13321-014-0044-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/08/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. RESULTS We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust. CONCLUSIONS The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.
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Affiliation(s)
- Ctibor Skuta
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic ; CZ-OPENSCREEN, Institute of Molecular Genetics of the ASCR, v. v. i, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Petr Bartůněk
- CZ-OPENSCREEN, Institute of Molecular Genetics of the ASCR, v. v. i, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic ; CZ-OPENSCREEN, Institute of Molecular Genetics of the ASCR, v. v. i, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
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12
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Nour A, Hayashi T, Chan M, Yao S, Tawatao RI, Crain B, Tsigelny IF, Kouznetsova VL, Ahmadiiveli A, Messer K, Pu M, Corr M, Carson DA, Cottam HB. Discovery of substituted 4-aminoquinazolines as selective Toll-like receptor 4 ligands. Bioorg Med Chem Lett 2014; 24:4931-8. [PMID: 25288184 DOI: 10.1016/j.bmcl.2014.09.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 01/23/2023]
Abstract
The Toll-like receptors (TLRs) are critical components of the innate immune system that regulate immune recognition in part through NF-κB activation. A human cell-based high throughput screen (HTS) revealed substituted 4-aminoquinazolines to be small molecular weight activators of NF-κB. The most potent hit compound predominantly stimulated through the human TLR4/MD2 complex, and had less activity with the mouse TLR4/MD2. There was no activity with other TLRs and the TLR4 activation was MD-2 dependent and CD14 independent. Synthetic modifications of the quinazoline scaffold at the 2 and 4 positions revealed trends in structure-activity relationships with respect to TLR dependent production of the NF-κB associated cytokine IL-8 in human peripheral blood mononuclear cells, as well as IL-6 in mouse antigen presenting cells. Furthermore, the hit compound in this series also activated the interferon signaling pathway resulting in type I interferon production. Substitution at the O-phenyl moiety with groups such as bromine, chlorine and methyl resulted in enhanced immunological activity. Computational studies indicated that the 4-aminoquinazoline compounds bind primarily to human MD-2 in the TLR4/MD-2 complex. These small molecules, which preferentially stimulate human rather than mouse innate immune cells, may be useful as adjuvants or immunotherapeutic agents.
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Affiliation(s)
- Afshin Nour
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Tomoko Hayashi
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Michael Chan
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Shiyin Yao
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Rommel I Tawatao
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Brian Crain
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Igor F Tsigelny
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States; San Diego Supercomputer Center, and University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Valentina L Kouznetsova
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States; San Diego Supercomputer Center, and University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Alast Ahmadiiveli
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Karen Messer
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Minya Pu
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Maripat Corr
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0663, United States
| | - Dennis A Carson
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
| | - Howard B Cottam
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States
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13
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Chan M, Hayashi T, Mathewson RD, Nour A, Hayashi Y, Yao S, Tawatao RI, Crain B, Tsigelny IF, Kouznetsova VL, Messer K, Pu M, Corr M, Carson DA, Cottam HB. Identification of substituted pyrimido[5,4-b]indoles as selective Toll-like receptor 4 ligands. J Med Chem 2013; 56:4206-23. [PMID: 23656327 PMCID: PMC3722616 DOI: 10.1021/jm301694x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
A cell-based
high-throughput screen to identify small molecular
weight stimulators of the innate immune system revealed substituted
pyrimido[5,4-b]indoles as potent NFκB activators.
The most potent hit compound selectively stimulated Toll-like receptor
4 (TLR4) in human and mouse cells. Synthetic modifications of the
pyrimido[5,4-b]indole scaffold at the carboxamide,
N-3, and N-5 positions revealed differential TLR4 dependent production
of NFκB and type I interferon associated cytokines, IL-6 and
interferon γ-induced protein 10 (IP-10) respectively. Specifically,
a subset of compounds bearing phenyl and substituted phenyl carboxamides
induced lower IL-6 release while maintaining higher IP-10 production,
skewing toward the type I interferon pathway. Substitution at N-5
with short alkyl substituents reduced the cytotoxicity of the leading
hit compound. Computational studies supported that active compounds
appeared to bind primarily to MD-2 in the TLR4/MD-2 complex. These
small molecules, which stimulate innate immune cells with minimal
toxicity, could potentially be used as adjuvants or immune modulators.
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Affiliation(s)
- Michael Chan
- Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0695, USA
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