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Sawada R, Sakajiri Y, Shibata T, Yamanishi Y. Predicting therapeutic and side effects from drug binding affinities to human proteome structures. iScience 2024; 27:110032. [PMID: 38868195 PMCID: PMC11167438 DOI: 10.1016/j.isci.2024.110032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/08/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
Evaluation of the binding affinities of drugs to proteins is a crucial process for identifying drug pharmacological actions, but it requires three dimensional structures of proteins. Herein, we propose novel computational methods to predict the therapeutic indications and side effects of drug candidate compounds from the binding affinities to human protein structures on a proteome-wide scale. Large-scale docking simulations were performed for 7,582 drugs with 19,135 protein structures revealed by AlphaFold (including experimentally unresolved proteins), and machine learning models on the proteome-wide binding affinity score (PBAS) profiles were constructed. We demonstrated the usefulness of the method for predicting the therapeutic indications for 559 diseases and side effects for 285 toxicities. The method enabled to predict drug indications for which the related protein structures had not been experimentally determined and to successfully extract proteins eliciting the side effects. The proposed method will be useful in various applications in drug discovery.
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Affiliation(s)
- Ryusuke Sawada
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yuko Sakajiri
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Japan
| | - Tomokazu Shibata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Japan
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Mumtaz S, Baseer N, Habib SH. Concomitant use of pre-emptive analgesia with local and general anesthesia in rat uterine pain surgical model. Mol Pain 2024; 20:17448069241252385. [PMID: 38631845 DOI: 10.1177/17448069241252385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Preemptive analgesia is used for postoperative pain management, providing pain relief with few adverse effects. In this study, the effect of a preemptive regime on rat behavior and c-fos expression in the spinal cord of the uterine surgical pain model was evaluated. It was a lab-based experimental study in which 60 female Sprague-Dawley rats; eight to 10 weeks old, weighing 150-300 gm were used. The rats were divided into two main groups: (i) superficial pain group (SG) (with skin incision only), (ii) deep pain group (with skin and uterine incisions). Each group was further divided into three subgroups based on the type of preemptive analgesia administered i.e., "tramadol, buprenorphine, and saline subgroups." Pain behavior was evaluated using the "Rat Grimace Scale" (RGS) at 2, 4, 6, 9 and 24 h post-surgery. Additionally, c-fos immunohistochemistry was performed on sections from spinal dorsal horn (T12-L2), and its expression was evaluated using optical density and mean cell count 2 hours postoperatively. Significant reduction in the RGS was noted in both the superficial and deep pain groups within the tramadol and buprenorphine subgroups when compared to the saline subgroup (p ≤ .05). There was a significant decrease in c-fos expression both in terms of number of c-fos positive cells and the optical density across the superficial laminae and lamina X of the spinal dorsal horn in both SD and DG (p ≤ .05). In contrast, the saline group exhibited c-fos expression primarily in laminae I-II and III-IV for both superficial and deep pain groups and lamina X in the deep pain group only (p ≤ .05). Hence, a preemptive regimen results in significant suppression of both superficial and deep components of pain transmission. These findings provide compelling evidence of the analgesic efficacy of preemptive treatment in alleviating pain response associated with uterine surgery.
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Affiliation(s)
- Saima Mumtaz
- Department of Anatomy, Federal Medical College Islamabad. Islamabad, Pakistan
| | - Najma Baseer
- Department of Anatomy, Institute of Basic Medical Science, Khyber Medical University, Peshawar, Pakistan
| | - Syed Hamid Habib
- Department of Physiology, Institute of Basic Medical Science, Khyber Medical University, Peshawar, Pakistan
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Kataria J, Kerr J, Lourenssen SR, Blennerhassett MG. Nintedanib regulates intestinal smooth muscle hyperplasia and phenotype in vitro and in TNBS colitis in vivo. Sci Rep 2022; 12:10275. [PMID: 35715562 PMCID: PMC9206006 DOI: 10.1038/s41598-022-14491-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Chronic inflammation of the human intestine in Crohn’s disease (CD) causes bowel wall thickening, which typically progresses to stricturing and a recurrent need for surgery. Current therapies have limited success and CD remains idiopathic and incurable. Recent evidence shows a key role of intestinal smooth muscle cell (ISMC) hyperplasia in stricturing, which is not targeted by current anti-inflammatory therapeutics. However, progression of idiopathic pulmonary fibrosis, resembling CD in pathophysiology, is controlled by the tyrosine kinase inhibitors nintedanib (NIN) or pirfenidone, and we investigated these drugs for their effect on ISMC. In a culture model of rat ISMC, NIN inhibited serum- and PDGF-BB-stimulated growth and cell migration, and promoted the differentiated phenotype, while increasing secreted collagen. NIN did not affect signaling through PDGF-Rβ or NFκB but did inhibit cytokine-induced expression of the pro-inflammatory cytokines IL-1β and TNFα, supporting a transcriptional level of control. In TNBS-induced colitis in mice, which resembles CD, NIN decreased ISMC hyperplasia as well as expression of TNFα and IL-1β, without effect in control animals. NIN also inhibited growth of human ISMC in response to human serum or PDGF-BB, which further establishes a broad range of actions of NIN that support further trial in human IBD.
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Affiliation(s)
- Jay Kataria
- Gastrointestinal Diseases Research Unit, Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Jack Kerr
- Gastrointestinal Diseases Research Unit, Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Sandra R Lourenssen
- Gastrointestinal Diseases Research Unit, Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Michael G Blennerhassett
- Gastrointestinal Diseases Research Unit, Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen's University, Kingston, ON, K7L 2V7, Canada.
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GDNF requires HIF-1α and RET activation for suppression of programmed cell death of enteric neurons by metabolic challenge. Mol Cell Neurosci 2021; 115:103655. [PMID: 34273501 DOI: 10.1016/j.mcn.2021.103655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/24/2021] [Accepted: 07/11/2021] [Indexed: 01/21/2023] Open
Abstract
Intestinal inflammation challenges both function and structure of the enteric nervous system (ENS). In the animal model of TNBS-induced colitis, an influx of immune cells causes early neuron death in the neuromuscular layers, followed by axonal outgrowth from surviving neurons associated with upregulation of the neurotrophin GDNF (glial cell line-derived neurotrophic factor). Inflammation could involve ischemia and metabolic inhibition leading to neuronal damage, which might be countered by a protective action of GDNF. This was examined in a primary co-culture model of rat myenteric neurons and smooth muscle, where metabolic challenge was caused by dinitrophenol (DNP), O-methyl glucose (OMG) or hypoxia. These caused the specific loss of 50% of neurons by 24 h that was blocked by GDNF both in vitro and in whole mounts. Neuroprotection was lost with RET inhibition by vandetanib or GSK3179106, which also caused neuron loss in untreated controls. Thus, both basal and upregulated GDNF levels signal via RET for neuronal survival. This includes a key role for upregulation of HIF-1α, which was detected in neurons in colitis, since the inhibitor chetomin blocked rescue by GDNF or ischemic pre-conditioning in vitro. In DNP-treated co-cultures, neuron death was not inhibited by zVAD, necrosulfonamide or GSK872, and cleaved caspase-3 or - 8 were undetectable. However, combinations of inhibitors or the RIP1kinase inhibitor Nec-1 prevented neuronal death, evidence for RIPK1-dependent necroptosis. Therefore, inflammation challenges enteric neurons via ischemia, while GDNF is neuroprotective, activating RET and HIF-1α to limit programmed cell death. This may support novel strategies to address recurrent inflammation in IBD.
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Blennerhassett MG, Lourenssen SR. Obligatory Activation of SRC and JNK by GDNF for Survival and Axonal Outgrowth of Postnatal Intestinal Neurons. Cell Mol Neurobiol 2021; 42:1569-1583. [PMID: 33544273 DOI: 10.1007/s10571-021-01048-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/22/2021] [Indexed: 01/20/2023]
Abstract
The neurotrophin GDNF acts through its co-receptor RET to direct embryonic development of the intestinal nervous system. Since this continues in the post-natal intestine, co-cultures of rat enteric neurons and intestinal smooth muscle cells were used to examine how receptor activation mediates neuronal survival or axonal extension. GDNF-mediated activation of SRC was essential for neuronal survival and axon outgrowth and activated the major downstream signaling pathways. Selective inhibition of individual pathways had little effect on survival but JNK activation was required for axonal maintenance, extension or regeneration. This was localized to axonal endings and retrograde transport was needed for central JUN activation and subsequent axon extension. Collectively, GDNF signaling supports neuronal survival via SRC activation with multiple downstream events, with JNK signaling mediating structural plasticity. These pathways may limit neuron death and drive subsequent regeneration during challenges in vivo such as intestinal inflammation, where supportive strategies could preserve intestinal function.
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Affiliation(s)
- M G Blennerhassett
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, ON, K7L 2V7, Canada.
- Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen's University, Kingston, ON, K7L2V7, Canada.
| | - S R Lourenssen
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, ON, K7L 2V7, Canada
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Pappritz K, Van Linthout S. Opioid-Induced Immunomodulation: Consequences for the Experimental Coxsackievirus B3-Induced Myocarditis Model. BIOLOGY 2020; 9:biology9100335. [PMID: 33066118 PMCID: PMC7650777 DOI: 10.3390/biology9100335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 01/18/2023]
Abstract
Simple Summary Myocarditis is an inflammatory disorder of the heart mainly caused by viruses. To investigate viral myocarditis, the Coxsackievirus B3 (CVB3)-induced myocarditis model is the experimental model used since more than sixty years. In the pathogeneses of viral myocarditis, the subtle balance between pro-and anti-inflammatory immune responses is of great importance for disease manifestation. Parallel to the infection of the heart, experimental CVB3-induced myocarditis results in an infection of the pancreas, causing a severe burden for the challenged animals. In frame of animal welfare, application of analgesics is mandatory. So far, positive as well as negative effects of opioids on the immune system have been described. However, the impact of opioid application on the pathogenesis of experimental CVB3-induced myocarditis has not been investigated yet. Since examinations on disease pathways and new treatment options rely on established models to generate reproducible data, applicability of opioids in experimental CVB3-induced myocarditis needs to be carefully evaluated. For this purpose, we summarized published studies for 13 different opioids and discussed their potential impact on the CVB3-induced myocarditis model. Abstract Myocarditis is an inflammatory disorder of the heart predominantly caused by infectious agents. Since more than sixty years, the Coxsackievirus B3 (CVB3)-induced myocarditis mouse model is the experimental model used to investigate viral myocarditis. The pathogenesis of viral myocarditis is conceptually a multiphase process, initiated by the infection of cardiomyocytes, followed by activation of the immune system, and resulting in myocardial fibrosis and left ventricular dysfunction. In parallel to the direct infection of the heart, CVB3 replicates in lymphatic organs such as the pancreas. Due to infection of the pancreas, the model of experimental CVB3-induced myocarditis is estimated as a severe burden for the challenged animals. Application of analgesics in frame of the animal welfare act (European directive 2010/63/EU) is more and more becoming a matter of debate. For this purpose, we summarized published studies for 13 different opioids and discussed their potential impact on CVB3-induced myocarditis. In addition, with this summary we also want to provide guidance for researchers beyond the myocarditis field to estimate the impact of opioids on the immune system for their specific model. In the literature, both immunosuppressive as well as immune-activating effects of opioids have been described, but examinations in experimental CVB3-induced myocarditis have still not been reported so far. Based on the existing publications, administration of opioids in experimental CVB3-induced myocarditis might result in more severe disease progression, including higher mortality, or a less pronounced myocarditis model, failing to be used for the establishment of new treatment options. Taken together, the applicability of opioids in experimental CVB3-induced myocarditis and in inflammatory models in general needs to be carefully evaluated and further investigated.
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Affiliation(s)
- Kathleen Pappritz
- Campus Virchow Klinikum (CVK), Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 10115 Berlin, Germany
- Correspondence: ; Tel.: +49-(0)30-450539509
| | - Sophie Van Linthout
- Campus Virchow Klinikum (CVK), Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 10115 Berlin, Germany
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Zoumboulakis D, Cirella KR, Gougeon PY, Lourenssen SR, Blennerhassett MG. MMP-9 Processing of Intestinal Smooth Muscle-derived GDNF is Required for Neurotrophic Action on Enteric Neurons. Neuroscience 2020; 443:8-18. [PMID: 32682824 DOI: 10.1016/j.neuroscience.2020.07.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 12/11/2022]
Abstract
The neurotrophin GDNF guides development of the enteric nervous system (ENS) in embryogenesis and directs survival and axon outgrowth in postnatal myenteric neurons in vitro. GDNF expression in intestinal smooth muscle cells is dynamic, with upregulation by inflammatory cytokines in vitro or intestinal inflammation in vivo, but the role of post-translational proteolytic cleavage is undefined. In a co-culture model of myenteric neurons, smooth muscle and glia, inhibition of serine or cysteine protease activity was ineffective against the >2-fold increase in axon density caused by TNFα. However, inhibitors of metalloproteinases (MMP) identified an essential role of MMP-9, and qPCR and western blotting showed that pro-inflammatory cytokines increased both mRNA and protein expression for MMP-9, in both cellular lysates and conditioned medium (CM). Inhibition of MMP-9 prevented the cytokine-induced increase in mature GDNF in CM or cellular lysates of co-cultures or cell lines of intestinal smooth muscle cells (ISMC) from adult rat colon. Western blotting showed parallel upregulation of mature GDNF and MMP-9 vs control in ISMC isolated on Day 2 of TNBS-induced colitis. Nonetheless, transfection of GDNF plasmid into HEK-293 cells as a carrier system, or directly into the co-culture model, conveyed a strong neurotrophic effect that was MMP-9 dependent. We conclude that MMP-9 activity is required for the neurotrophic effects of GDNF on myenteric neurons in vitro. However, the coordinated upregulation of GDNF and MMP-9 in intestinal smooth muscle by inflammatory cytokines provides a supportive, target cell-derived environment that limits inflammatory damage to the ENS.
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Affiliation(s)
- Demetri Zoumboulakis
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, ON K7L 2V7, Canada
| | - Kirsten R Cirella
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, ON K7L 2V7, Canada
| | - Pierre-Yves Gougeon
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, ON K7L 2V7, Canada
| | - Sandra R Lourenssen
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, ON K7L 2V7, Canada
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Lourenssen SR, Blennerhassett MG. M2 Macrophages and Phenotypic Modulation of Intestinal Smooth Muscle Cells Characterize Inflammatory Stricture Formation in Rats. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1843-1858. [PMID: 32479820 DOI: 10.1016/j.ajpath.2020.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
The progression of Crohn disease to intestinal stricture formation is poorly controlled, and the pathogenesis is unclear, although increased smooth muscle mass is present. A previously described rat model of trinitrobenzenesulfonic acid-induced colitis is re-examined here. Although inflammation of the mid-descending colon typically resolved, a subset showed characteristic stricturing by day 16, with an inflammatory infiltrate in the neuromuscular layers including eosinophils, CD3-positive T cells, and CD68-positive macrophages. Closer study identified CD163-positive, CD206-positive, and arginase-positive cells, indicating a M2 macrophage phenotype. Stricturing involved ongoing proliferation of intestinal smooth muscle cells (ISMC) with expression of platelet-derived growth factor receptor beta and progressive loss of phenotypic markers, and stable expression of hypoxia inducible factor 1 subunit alpha. In parallel, collagen I and III showed a selective and progressive increase over time. A culture model of the stricture phenotype of ISMC showed stable hypoxia inducible factor 1 subunit alpha expression that promoted growth and improved both survival and growth in models of experimental ischemia. This phenotype was hyperproliferative to serum and platelet-derived growth factor BB, and unresponsive to transforming growth factor beta, a prominent cytokine of M2 macrophages, compared with control ISMC. We identified a hyperplastic phenotype of ISMC, uniquely adapted to an ischemic environment to drive smooth muscle layer expansion, which may reveal new targets for treating intestinal fibrosis.
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Affiliation(s)
- Sandra R Lourenssen
- Gastrointestinal Diseases Research Unit and Queen's University, Kingston, Ontario, Canada
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Smith JC. A Review of Strain and Sex Differences in Response to Pain and Analgesia in Mice. Comp Med 2019; 69:490-500. [PMID: 31822324 DOI: 10.30802/aalas-cm-19-000066] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pain and its alleviation are currently a highly studied issue in human health. Research on pain and response to analgesia has evolved to include the effects of genetics, heritability, and sex as important components in both humans and animals. The laboratory mouse is the major animal studied in the field of pain and analgesia. Studying the inbred mouse to understand how genetic heritable traits and/or sex influence pain and analgesia has added valuable information to the complex nature of pain as a human disease. In the context of biomedical research, identifying pain and ensuring its control through analgesia in research animals remains one of the hallmark responsibilities of the research community. Advancements in both human and mouse genomic research shed light not only on the need to understand how both strain and sex affect the mouse pain response but also on how these research achievements can be used to improve the humane use of all research animal species. A better understanding of how strain and sex affect the response to pain may allow researchers to improve study design and thereby the reproducibility of animal research studies. The need to use both sexes, along with an improved understanding of how genetic heritability affects nociception and analgesic sensitivity, remains a key priority for pain researchers working with mice. This review summarizes the current literature on how strain and sex alter the response to pain and analgesia in the modern research mouse, and highlights the importance of both strain and sex selection in pain research.
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Affiliation(s)
- Jennifer C Smith
- Department of Bioresources, Henry Ford Health System, Detroit, Michigan;,
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DeMarco GJ, Nunamaker EA. A Review of the Effects of Pain and Analgesia on Immune System Function and Inflammation: Relevance for Preclinical Studies. Comp Med 2019; 69:520-534. [PMID: 31896389 PMCID: PMC6935697 DOI: 10.30802/aalas-cm-19-000041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
One of the most significant challenges facing investigators, laboratory animal veterinarians, and IACUCs, is how to balance appropriate analgesic use, animal welfare, and analgesic impact on experimental results. This is particularly true for in vivo studies on immune system function and inflammatory disease. Often times the effects of analgesic drugs on a particular immune function or model are incomplete or don't exist. Further complicating the picture is evidence of the very tight integration and bidirectional functionality between the immune system and branches of the nervous system involved in nociception and pain. These relationships have advanced the concept of understanding pain as a protective neuroimmune function and recognizing pathologic pain as a neuroimmune disease. This review strives to summarize extant literature on the effects of pain and analgesia on immune system function and inflammation in the context of preclinical in vivo studies. The authors hope this work will help to guide selection of analgesics for preclinical studies of inflammatory disease and immune system function.
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Key Words
- cb,endocannabinoid receptor
- cd,crohn disease
- cfa, complete freund adjuvant
- cgrp,calcitonin gene-related peptide
- cox,cyclooxygenase
- ctl, cytotoxic t-lymphocytes
- damp,damage-associated molecular pattern molecules
- drg,dorsal root ganglion
- dss, dextran sodium sulphate
- ecs,endocannabinoid system
- ibd, inflammatory bowel disease
- ifa,incomplete freund adjuvant
- las, local anesthetics
- pamp,pathogen-associated molecular pattern molecules
- pge2, prostaglandin e2
- p2y, atp purine receptor y
- p2x, atp purine receptor x
- tnbs, 2,4,6-trinitrobenzene sulphonic acid
- trp, transient receptor potential ion channels
- trpv, transient receptor potential vanilloid
- tg,trigeminal ganglion
- uc,ulcerative colitis
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Affiliation(s)
- George J DeMarco
- Department of Animal Medicine, University of Massachusetts Medical School, Worcester, Massachusetts;,
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