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Lau TA, Mair E, Rabbitts BM, Lohith A, Lokey RS. High-Content Image-Based Screening and Deep Learning for the Detection of Anti-Inflammatory Drug Leads. Chembiochem 2024; 25:e202300136. [PMID: 37815526 PMCID: PMC11126213 DOI: 10.1002/cbic.202300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
We developed a high-content image-based screen that utilizes the pro-inflammatory stimulus lipopolysaccharide (LPS) and murine macrophages (RAW264.7) with the goal of enabling the identification of novel anti-inflammatory lead compounds. We screened 2,259 bioactive compounds with annotated mechanisms of action (MOA) to identify compounds that block the LPS-induced phenotype in macrophages. We utilized a set of seven fluorescence microscopy probes to generate images that were used to train and optimize a deep neural network classifier to distinguish between unstimulated and LPS-stimulated macrophages. The top hits from the deep learning classifier were validated using a linear classifier trained on individual cells and subsequently investigated in a multiplexed cytokine secretion assay. All 12 hits significantly modulated the expression of at least one cytokine upon LPS stimulation. Seven of these were allosteric inhibitors of the mitogen-activated protein kinase kinase (MEK1/2) and showed similar effects on cytokine expression. This deep learning morphological assay identified compounds that modulate the innate immune response to LPS and may aid in identifying new anti-inflammatory drug leads.
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Affiliation(s)
- Tannia A Lau
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Elmar Mair
- No affiliation, Santa Cruz, CA 95060, USA
| | - Beverley M Rabbitts
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Akshar Lohith
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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2
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Onyedibe KI, Mohallem R, Wang M, Aryal UK, Sintim HO. Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2'3' cGAMP reveals various signaling axes impacted by cyclic dinucleotides. J Proteomics 2023; 279:104869. [PMID: 36889538 DOI: 10.1016/j.jprot.2023.104869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
Cyclic dinucleotides (CDNs), such as 2'3'-cGAMP, bind to STING to trigger the production of cytokines and interferons, mainly via activation of TBK1. STING activation by CDN also leads to the release and activation of Nuclear Factor Kappa-light-chain-enhancer of activated B cells (NF-κB) via the phosphorylation of Inhibitor of NF-κB (IκB)-alpha (IκBα) by IκB Kinase (IKK). Beyond the canonical TBK1 or IKK phosphorylations, little is known about how CDNs broadly affect the phosphoproteome and/or other signaling axes. To fill this gap, we performed an unbiased proteome and phosphoproteome analysis of Jurkat T-cell treated with 2'3'-cGAMP or vehicle control to identify proteins and phosphorylation sites that are differentially modulated by 2'3'-cGAMP. We uncovered different classes of kinase signatures associated with cell response to 2'3'-cGAMP. 2'3'-cGAMP upregulated Arginase 2 (Arg2) and the antiviral innate immune response receptor RIG-I as well as proteins involved in ISGylation, E3 ISG15-protein ligase HERC5 and ubiquitin-like protein ISG15, while downregulating ubiquitin-conjugating enzyme UBE2C. Kinases that play a role in DNA double strand break repair, apoptosis, and cell cycle regulation were differentially phosphorylated. Overall, this work demonstrates that 2'3'-cGAMP has a much broader effects on global phosphorylation events than currently appreciated, beyond the canonical TBK1/IKK signaling. SIGNIFICANCE: The host cyclic dinucleotide, 2'3'-cGAMP is known to bind to Stimulator of Interferon Genes (STING) to trigger the production of cytokines and interferons in immune cells via STING-TBK1-IRF3 pathway. Beyond the canonical phosphorelay via the STING-TBK1-IRF3 pathway, little is known about how this second messenger broadly affects the global proteome. Using an unbiased phosphoproteomics, this study identifies several kinases and phosphosites that are modulated by cGAMP. The study expands our knowledge about how cGAMP modulates global proteome and also global phosphorylations.
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Affiliation(s)
- Kenneth I Onyedibe
- Department of Chemistry, Purdue University, West Lafayette, IN, USA; Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Rodrigo Mohallem
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Modi Wang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Uma K Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, West Lafayette, IN, USA; Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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3
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Niu J, Bai H, Li Z, Gao Y, Zhang Y, Wang X, Yang Y, Xu Y, Geng M, Xie Z, Zhou B. Discovery of novel Thieno[2,3-d]imidazole derivatives as agonists of human STING for antitumor immunotherapy using systemic administration. Eur J Med Chem 2022; 238:114482. [DOI: 10.1016/j.ejmech.2022.114482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
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Zhang Q, Chen C, Xia B, Xu P. Chemical regulation of the cGAS-STING pathway. Curr Opin Chem Biol 2022; 69:102170. [PMID: 35753220 DOI: 10.1016/j.cbpa.2022.102170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
Nucleic acids represent a major class of pathogen and damage signatures, recognized by a variety of host sensors to initiate signaling cascades and immune responses, such as mechanisms of RLR-MAVS, cGAS-STING, TLR-TRIF, and AIM2 inflammasome. Yet, an outstanding challenge is understanding how nucleic acid sensing initiates immune responses and its tethering in various infectious, cancerous, autoimmune, and inflammatory diseases. However, the discovery and application of a plethora of small molecule compounds have substantially facilitated this process. This review provides an overview and recent development of the innate DNA-sensing pathway of cGAS-STING and highlights the multiple agonists and inhibitors in fine-tuning the pathway that can be exploited to improve disease treatment, focusing primarily on crucial pathway components and regulators.
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Affiliation(s)
- Qian Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chen Chen
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Bing Xia
- Department of Thoracic Cancer, Affiliated Hangzhou Cancer Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Pinglong Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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5
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Ng TL, Olson EJ, Yoo TY, Weiss HS, Koide Y, Koch PD, Rollins NJ, Mach P, Meisinger T, Bricken T, Chang TZ, Molloy C, Zürcher J, Chang RL, Mitchison TJ, Glass JI, Marks DS, Way JC, Silver PA. High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response. mSystems 2022; 7:e0146621. [PMID: 35319251 PMCID: PMC9040872 DOI: 10.1128/msystems.01466-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/21/2022] [Indexed: 11/20/2022] Open
Abstract
Suppression of the host innate immune response is a critical aspect of viral replication. Upon infection, viruses may introduce one or more proteins that inhibit key immune pathways, such as the type I interferon pathway. However, the ability to predict and evaluate viral protein bioactivity on targeted pathways remains challenging and is typically done on a single-virus or -gene basis. Here, we present a medium-throughput high-content cell-based assay to reveal the immunosuppressive effects of viral proteins. To test the predictive power of our approach, we developed a library of 800 genes encoding known, predicted, and uncharacterized human virus genes. We found that previously known immune suppressors from numerous viral families such as Picornaviridae and Flaviviridae recorded positive responses. These include a number of viral proteases for which we further confirmed that innate immune suppression depends on protease activity. A class of predicted inhibitors encoded by Rhabdoviridae viruses was demonstrated to block nuclear transport, and several previously uncharacterized proteins from uncultivated viruses were shown to inhibit nuclear transport of the transcription factors NF-κB and interferon regulatory factor 3 (IRF3). We propose that this pathway-based assay, together with early sequencing, gene synthesis, and viral infection studies, could partly serve as the basis for rapid in vitro characterization of novel viral proteins. IMPORTANCE Infectious diseases caused by viral pathogens exacerbate health care and economic burdens. Numerous viral biomolecules suppress the human innate immune system, enabling viruses to evade an immune response from the host. Despite our current understanding of viral replications and immune evasion, new viral proteins, including those encoded by uncultivated viruses or emerging viruses, are being unearthed at a rapid pace from large-scale sequencing and surveillance projects. The use of medium- and high-throughput functional assays to characterize immunosuppressive functions of viral proteins can advance our understanding of viral replication and possibly treatment of infections. In this study, we assembled a large viral-gene library from diverse viral families and developed a high-content assay to test for inhibition of innate immunity pathways. Our work expands the tools that can rapidly link sequence and protein function, representing a practical step toward early-stage evaluation of emerging and understudied viruses.
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Affiliation(s)
- Tai L. Ng
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Erika J. Olson
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Tae Yeon Yoo
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - H. Sloane Weiss
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Yukiye Koide
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Peter D. Koch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Nathan J. Rollins
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Pia Mach
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Tobias Meisinger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Trenton Bricken
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Timothy Z. Chang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Colin Molloy
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Jérôme Zürcher
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Roger L. Chang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Timothy J. Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - John I. Glass
- J. Craig Venter Institute, La Jolla, California, USA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C. Way
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Zhang YY, Yao YD, Cheng QQ, Huang YF, Zhou H. Establishment of a High Content Image Platform to Measure NF-κB Nuclear Translocation in LPS-Induced RAW264.7 Macrophages for Screening Anti-inflammatory Drug Candidates. Curr Drug Metab 2022; 23:394-414. [PMID: 35410593 DOI: 10.2174/1389200223666220411121614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 01/19/2022] [Accepted: 01/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND High content image (HCI), an automatic imaging and analysis system, provides a fast drug screening method by detecting the subcellular distribution of protein in intact cells. OBJECTIVE This study established the first standardized HCI platform for lipopolysaccharide (LPS)-induced RAW264.7 macrophages to screen anti-inflammatory compounds by measuring nuclear factor-κB (NF-κB) nuclear translocation. METHOD The influence of the cell passages, cell density, LPS induction time and concentration, antibody dilution, serum, dimethyl sulfoxide and analysis parameters on NF-κB nuclear translocation and HCI data quality was optimized. The BAY-11-7085, the positive control for inhibiting NF-κB and Western blot assay were separately employed to verify the stability and reliability of the platform. Lastly, the effect of BHA on NO release, iNOS expression, IL-1β, IL-6, and TNF-α mRNA in LPS-induced RAW264.7 cells was detected. RESULTS The optimal conditions for measuring NF-κB translocation in LPS-induced RAW264.7 cells by HCI were established. Cells that do not exceed 22 passages were seeded at a density of 10 k cells/well and pretreated with compounds following 200 ng/mL LPS for 40 min. Parameters including nuclear area of 65 μm2, cell area of 80 μm2, collar of 0.9 μm and sensitivity of 25% were recommended for image segmentation algorithms in the analysis workstation. Benzoylhypaconine from aconite was screened for the first time as an anti-inflammatory candidate by the established HCI platform. The inhibitory effect of benzoylhypaconine on NF-κB translocation was verified by Western blot. Furthermore, benzoylhypaconine reduced the release of NO, inhibited the expression of iNOS, decreased the mRNA levels of IL-1β, IL-6, and TNF-α. CONCLUSION The established HCI platform could be applied to screen anti-inflammatory compounds by measuring the NF-κB nuclear translocation in LPS-induced RAW264.7 cells.
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Affiliation(s)
- Yan-Yu Zhang
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, P.R. China.,Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
| | - Yun-Da Yao
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, P.R. China.,Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
| | - Qi-Qing Cheng
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, P.R. China.,Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
| | - Yu-Feng Huang
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, P.R. China.,Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
| | - Hua Zhou
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, P.R. China.,Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China.,Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, Zhuhai City, Guangdong Province 519000, P.R. China
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7
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Yu TT, Sang XY, Han N, Peng XC, Li QR, Xu X, Xiao RC, Xu HZ, Chen X, Wang MF, Li TF. Macrophages mediated delivery of chlorin e6 and treatment of lung cancer by photodynamic reprogramming. Int Immunopharmacol 2021; 100:108164. [PMID: 34562845 DOI: 10.1016/j.intimp.2021.108164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022]
Abstract
Photodynamic therapy (PDT) is an emerging anti-tumor strategy.Photosensitizer chlorin e6 (Ce6) can induce photodynamic effect to selectively damage lung cancer cells.In order to further improve its tumor targeting ability, macrophages can be applied as carrier to deliver Ce6 to lung cancer.Tumor associated macrophages (TAM) are important immunocytes in lung cancer immune microenvironment. TAM play crucial role in tumor promotion due to the Immunosuppressive property, reprogramming phenotype of TAM therefore has become a promising strategy.Based on this, in the present study, we suppose that TAM can be used as carrier to deliver Ce6 to lung cancer and be reprogrammed to M1 phenotype by photodynamic action to mediate anti-lung cancer efficacy.The results showed TAM could load with Ce6 and keep viability in the absence of near infrared irradiation (NIR).Moreover, Its viability decreased little within 10 h after NIR.Ce6-loaded TAM could deliver Ce6 to lung cancer cells and retain some drugs in TAM per se.After NIR, phagocytosis of macrophages was enhanced. The expressions of GBP5, iNOS and MHC-II was up-regulated, which indicated TAM were polarized to M1 phenotype.Finally, the study also found the reprogrammed macrophages could inhibit the proliferation and promote the apoptosis of lung cancer cells.These results suggested that macrophages could deliver Ce6 to lung cancer and exhibit anti-lung cancer effect through photodynamic reprogramming.This study provides a novel approach for combining photodynamic action with anti-tumor immunotherapy.
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Affiliation(s)
- Ting-Ting Yu
- Department of respiratory, Taihe Hospital of Shiyan, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Xue-Yu Sang
- Department of respiratory, Taihe Hospital of Shiyan, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Ning Han
- Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Xing-Chun Peng
- Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Qi-Rui Li
- Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Xiang Xu
- Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Rong-Cheng Xiao
- Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Hua-Zhen Xu
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Avenue No.185, Wuhan 430072, China
| | - Xiao Chen
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Avenue No.185, Wuhan 430072, China
| | - Mei-Fang Wang
- Department of respiratory, Taihe Hospital of Shiyan, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China.
| | - Tong-Fei Li
- Department of respiratory, Taihe Hospital of Shiyan, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China.
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Chen L, Zhao S, Zhu Y, Liu Y, Li H, Zhao Q. Molecular Dynamics Simulations Reveal the Modulated Mechanism of STING Conformation. Interdiscip Sci 2021; 13:751-765. [PMID: 34142362 DOI: 10.1007/s12539-021-00446-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
Stimulator of interferon genes (STING), which is an integral ER-membrane protein, could induce an antiviral state and boost antitumor immunity. Recent experiments reported that different small molecules could modulate the conformation of the STING. However, the mechanism of small molecules modulating the conformation of STING is still unknown. To illustrate the conformational modulated mechanism of STING by small molecules at atomic level, we investigated the interactions between STING and the small molecules: cGAMP and diABZI with molecular dynamics (MD) simulations method. Interestingly, we found that the residues of STING in the binding pocket are more flexible in the monomers of STING than that in the dimer of STING. We also demonstrated that cGAMP and diABZI have a similar binding mode to STING monomers/dimer, and π-π stacking interactions play important roles for the agonists and STING. Our study proposed mechanistic insights into the STING conformation modulated by small molecules and we suggested that the special molecule (e. g. diABZI) could induce the conformational transition of STING from the "open" monomers to the "closed" dimer state. Our research may provide a clue for the development of cancer immunotherapy.
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Affiliation(s)
- Li Chen
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Shuang Zhao
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Yongsheng Liu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China.
| | - Qingjie Zhao
- Shanghai Institute of Material Medical, Chinese Academy of Sciences, Shanghai, 201203, China.
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Malandraki-Miller S, Riley PR. Use of artificial intelligence to enhance phenotypic drug discovery. Drug Discov Today 2021; 26:887-901. [PMID: 33484947 DOI: 10.1016/j.drudis.2021.01.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/28/2020] [Accepted: 01/15/2021] [Indexed: 01/17/2023]
Abstract
Research and development (R&D) productivity across the pharmaceutical industry has received close scrutiny over the past two decades, especially taking into consideration reports of attrition rates and the colossal cost for drug development. The respective merits of the two main drug discovery approaches, phenotypic and target based, have divided opinion across the research community, because each hold different advantages for identifying novel molecular entities with a successful path to the market. Nevertheless, both have low translatability in the clinic. Artificial intelligence (AI) and adoption of machine learning (ML) tools offer the promise of revolutionising drug development, and overcoming obstacles in the drug discovery pipeline. Here, we assess the potential of target-driven and phenotypic-based approaches and offer a holistic description of the current state of the field, from both a scientific and industry perspective. With the emerging partnerships between AI/ML and pharma still in their relative infancy, we investigate the potential and current limitations with a particular focus on phenotypic drug discovery. Finally, we emphasise the value of public-private partnerships (PPPs) and cross-disciplinary collaborations to foster innovation and facilitate efficient drug discovery programmes.
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Affiliation(s)
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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10
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Pasquer QTL, Tsakoumagkos IA, Hoogendoorn S. From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems. Molecules 2020; 25:E5702. [PMID: 33287212 PMCID: PMC7730769 DOI: 10.3390/molecules25235702] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/22/2023] Open
Abstract
Biologically active small molecules have a central role in drug development, and as chemical probes and tool compounds to perturb and elucidate biological processes. Small molecules can be rationally designed for a given target, or a library of molecules can be screened against a target or phenotype of interest. Especially in the case of phenotypic screening approaches, a major challenge is to translate the compound-induced phenotype into a well-defined cellular target and mode of action of the hit compound. There is no "one size fits all" approach, and recent years have seen an increase in available target deconvolution strategies, rooted in organic chemistry, proteomics, and genetics. This review provides an overview of advances in target identification and mechanism of action studies, describes the strengths and weaknesses of the different approaches, and illustrates the need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes.
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Affiliation(s)
| | | | - Sascha Hoogendoorn
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Genève, Switzerland; (Q.T.L.P.); (I.A.T.)
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11
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Canham SM, Wang Y, Cornett A, Auld DS, Baeschlin DK, Patoor M, Skaanderup PR, Honda A, Llamas L, Wendel G, Mapa FA, Aspesi P, Labbé-Giguère N, Gamber GG, Palacios DS, Schuffenhauer A, Deng Z, Nigsch F, Frederiksen M, Bushell SM, Rothman D, Jain RK, Hemmerle H, Briner K, Porter JA, Tallarico JA, Jenkins JL. Systematic Chemogenetic Library Assembly. Cell Chem Biol 2020; 27:1124-1129. [PMID: 32707038 DOI: 10.1016/j.chembiol.2020.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/03/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022]
Abstract
Chemogenetic libraries, collections of well-defined chemical probes, provide tremendous value to biomedical research but require substantial effort to ensure diversity as well as quality of the contents. We have assembled a chemogenetic library by data mining and crowdsourcing institutional expertise. We are sharing our approach, lessons learned, and disclosing our current collection of 4,185 compounds with their primary annotated gene targets (https://github.com/Novartis/MoaBox). This physical collection is regularly updated and used broadly both within Novartis and in collaboration with external partners.
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Affiliation(s)
- Stephen M Canham
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Yuan Wang
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Allen Cornett
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Douglas S Auld
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Daniel K Baeschlin
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Maude Patoor
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philip R Skaanderup
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ayako Honda
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Luis Llamas
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Greg Wendel
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Peter Aspesi
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nancy Labbé-Giguère
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gabriel G Gamber
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Daniel S Palacios
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ansgar Schuffenhauer
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Zhan Deng
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Florian Nigsch
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Mathias Frederiksen
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Simon M Bushell
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Deborah Rothman
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rishi K Jain
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Horst Hemmerle
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Karin Briner
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeffery A Porter
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeremy L Jenkins
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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12
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Awan Z, Kutbi HI, Ahmad A, Syed R, Alsulaimany FAS, Shaik NA. Molecular design, synthesis and biological characterization of novel Resveratrol derivative as potential anticancer agent targeting NF-κB. J Appl Biomed 2020; 18:8-17. [PMID: 34907703 DOI: 10.32725/jab.2020.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/23/2020] [Indexed: 11/05/2022] Open
Abstract
Resveratrol (RESV), an anticancer nutraceutical compound, is known to show poor bioavailability inside the human body. Therefore, this study has designed multiple chemical analogs of RESV compound for improving its pharmacokinetic as well as its anti-cancer properties. Initially, the drug likeliness and ADME-toxicity properties of these new chemical analogs were tested with the help of diverse computational approaches. Then the best predicted RESV derivative is synthesized by the organic method, and its NF-κB mediated anti-tumor activity assessed on histiocytic lymphoma U-937 cells. The new synthetic RESV analog, i.e. (E)-3-(prop-2-yn-1-yloxy)-5-(4-(prop-2-yn-1-yloxy) styryl) phenol has shown a rapid, persistent and better dose-dependent (IC50 of 7.25 μM) decrease in the viability of U937 cells than the native (IC50 of 30 μM) RESV compound. This analog has also demonstrated its potential ability in inducing apoptosis through DNA ladder formation. At 10 µg/ml concentration, this chemical derivative has shown a better NF-κB inhibition (IC50 is 2.45) compared to the native RESV compound (IC50 is 1.95). Molecular docking analysis found that this analog exerts its anti- NF-κB activity (binding energy of -6.78 kcal/mol and Ki 10 µM) by interacting with DNA binding residues (Arg246, Lys444, and Gln606) of p50 chain NF-κB. This study presents a novel RESV analog that could further develop as a potential anti-NF-κB mediated tumor inhibitor.
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Affiliation(s)
- Zuhier Awan
- King Abdulaziz University, Faculty of Medicine, Department of Clinical Biochemistry, Jeddah, Kingdom of Saudi Arabia
| | - Hussam Ibrahim Kutbi
- King Abdulaziz University, Faculty of Pharmacy, Department of Pharmacy Practice, Jeddah, Kingdom of Saudi Arabia
| | - Aftab Ahmad
- King Abdulaziz University, Faculty of Applied Studies, Health Information Technology Department, Jedah, Kingdom of Saudi Arabia
| | - Rabbani Syed
- King Saud University, College of Pharmacy, Department of Pharmaceutics, Riyadh, Kingdom of Saudi Arabia
| | - Faten A S Alsulaimany
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Jeddah, Kingdom of Saudi Arabia
| | - Noor Ahmad Shaik
- King Abdulaziz University, Faculty of Medicine, Department of Genetic Medicine, Jeddah, Kingdom of Saudi Arabia.,King Abdulaziz University, "Princess Al-Jawhara, Al-Brahim Center of Excellence in Research of Hereditary Disorders", Jeddah, Kingdom of Saudi Arabia
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13
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Mazumdar C, Driggers EM, Turka LA. The Untapped Opportunity and Challenge of Immunometabolism: A New Paradigm for Drug Discovery. Cell Metab 2020; 31:26-34. [PMID: 31839485 DOI: 10.1016/j.cmet.2019.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 10/24/2019] [Accepted: 11/14/2019] [Indexed: 12/14/2022]
Abstract
Here, we explore the manipulation of immune cell metabolism as a strategy in target discovery and drug development for immune-mediated diseases. Comparing exploitation of metabolic pathways to kill tumor cells for cancer treatment with the reprogramming of immune cells to treat autoimmune diseases highlights differences that confer several advantages to the latter (including a more favorable therapeutic index and greater target stability). We discuss technological capabilities and gaps, including the challenge of relating in vitro observations to in vivo biology. Finally, we conclude by identifying future opportunities that will move the field forward and accelerate drug discovery.
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14
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MGL1 Receptor Plays a Key Role in the Control of T. cruzi Infection by Increasing Macrophage Activation through Modulation of ERK1/2, c-Jun, NF-κB and NLRP3 Pathways. Cells 2020; 9:cells9010108. [PMID: 31906385 PMCID: PMC7017267 DOI: 10.3390/cells9010108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Macrophage galactose-C type lectin (MGL)1 receptor is involved in the recognition of Trypanosoma cruzi (T. cruzi) parasites and is important for the modulation of the innate and adaptive immune responses. However, the mechanism by which MGL1 promotes resistance to T. cruzi remains unclear. Here, we show that MGL1 knockout macrophages (MGL1-/- Mφ) infected in vitro with T. cruzi were heavily parasitized and showed decreased levels of reactive oxygen species (ROS), nitric oxide (NO), IL-12 and TNF-α compared to wild-type macrophages (WT Mφ). MGL1-/- Mφ stimulated in vitro with T. cruzi antigen (TcAg) showed low expression of TLR-2, TLR-4 and MHC-II, which resulted in deficient splenic cell activation compared with similar co-cultured WT Mφ. Importantly, the activation of p-ERK1/2, p-c-Jun and p-NF-κB p65 were significantly reduced in MGL1-/- Mφ exposed to TcAg. Similarly, procaspase 1, caspase 1 and NLRP3 inflammasome also displayed a reduced expression that was associated with low IL-β production. Our data reveal a previously unappreciated role for MGL1 in Mφ activation through the modulation of ERK1/2, c-Jun, NF-κB and NLRP3 signaling pathways, and to the development of protective innate immunity against experimental T. cruzi infection.
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15
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Sintim HO, Mikek CG, Wang M, Sooreshjani MA. Interrupting cyclic dinucleotide-cGAS-STING axis with small molecules. MEDCHEMCOMM 2019; 10:1999-2023. [PMID: 32206239 PMCID: PMC7069516 DOI: 10.1039/c8md00555a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
The cyclic dinucleotide-cGAS-STING axis plays important roles in host immunity. Activation of this signaling pathway, via cytosolic sensing of bacterial-derived c-di-GMP/c-di-AMP or host-derived cGAMP, leads to the production of inflammatory interferons and cytokines that help resolve infection. Small molecule activators of the cGAS-STING axis have the potential to augment immune response against various pathogens or cancer. The aberrant activation of this pathway, due to gain-of-function mutations in any of the proteins that are part of the signaling axis, could lead to various autoimmune diseases. Inhibiting various nodes of the cGAS-STING axis could provide relief to patients with autoimmune diseases. Many excellent reviews on the cGAS-STING axis have been published recently, and these have mainly focused on the molecular details of the cGAS-STING pathway. This review however focuses on small molecules that can be used to modulate various aspects of the cGAS-STING pathway, as well as other parallel inflammatory pathways.
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Affiliation(s)
- Herman O Sintim
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Institute for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
- Purdue Institute of Inflammation and Infectious Diseases , Purdue University , West Lafayette , IN 47907 , USA
| | - Clinton G Mikek
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
| | - Modi Wang
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
| | - Moloud A Sooreshjani
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
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16
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Rodell CB, Koch PD, Weissleder R. Screening for new macrophage therapeutics. Theranostics 2019; 9:7714-7729. [PMID: 31695796 PMCID: PMC6831478 DOI: 10.7150/thno.34421] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Myeloid derived macrophages play a key role in many human diseases, and their therapeutic modulation via pharmacological means is receiving considerable attention. Of particular interest is the fact that these cells are i) dynamic phenotypes well suited to therapeutic manipulation and ii) phagocytic, allowing them to be efficiently targeted with nanoformulations. However, it is important to consider that macrophages represent heterogeneous populations of subtypes with often competing biological behaviors and functions. In order to develop next generation therapeutics, it is therefore essential to screen for biological effects through a combination of in vitro and in vivo assays. Here, we review the state-of-the-art techniques, including both cell based screens and in vivo imaging tools that have been developed for assessment of macrophage phenotype. We conclude with a forward-looking perspective on the growing need for noninvasive macrophage assessment and laboratory assays to be put into clinical practice and the potential broader impact of myeloid-targeted therapeutics.
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17
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Siu T, Altman MD, Baltus GA, Childers M, Ellis JM, Gunaydin H, Hatch H, Ho T, Jewell J, Lacey BM, Lesburg CA, Pan BS, Sauvagnat B, Schroeder GK, Xu S. Discovery of a Novel cGAMP Competitive Ligand of the Inactive Form of STING. ACS Med Chem Lett 2019; 10:92-97. [PMID: 30655953 DOI: 10.1021/acsmedchemlett.8b00466] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022] Open
Abstract
Drugging large protein pockets is a challenge due to the need for higher molecular weight ligands, which generally possess undesirable physicochemical properties. In this communication, we highlight a strategy leveraging small molecule active site dimers to inhibit the large symmetric binding pocket in the STING protein. By taking advantage of the 2:1 binding stoichiometry, maximal buried interaction with STING protein can be achieved while maintaining the ligand physicochemical properties necessary for oral exposure. This mode of binding requires unique considerations for potency optimization including simultaneous optimization of protein-ligand as well as ligand-ligand interactions. Successful implementation of this strategy led to the identification of 18, which exhibits good oral exposure, slow binding kinetics, and functional inhibition of STING-mediated cytokine release.
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18
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Tang D, Kang R. Response to comment on "ALK is a therapeutic target for lethal sepsis". Sci Transl Med 2018; 10:10/471/eaas9817. [PMID: 30541792 DOI: 10.1126/scitranslmed.aas9817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 11/09/2018] [Indexed: 11/02/2022]
Abstract
ALK inhibitors may exhibit STING-independent anti-inflammatory activity in macrophages and monocytes.
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Affiliation(s)
- Daolin Tang
- The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510510, China. .,Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA.,Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rui Kang
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA.,Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
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