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Disease-related compound identification based on deeping learning method. Sci Rep 2022; 12:20594. [PMID: 36446871 PMCID: PMC9708143 DOI: 10.1038/s41598-022-24385-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022] Open
Abstract
Acute lung injury (ALI) is a serious respiratory disease, which can lead to acute respiratory failure or death. It is closely related to the pathogenesis of New Coronavirus pneumonia (COVID-19). Many researches showed that traditional Chinese medicine (TCM) had a good effect on its intervention, and network pharmacology could play a very important role. In order to construct "disease-gene-target-drug" interaction network more accurately, deep learning algorithm is utilized in this paper. Two ALI-related target genes (REAL and SATA3) are considered, and the active and inactive compounds of the two corresponding target genes are collected as training data, respectively. Molecular descriptors and molecular fingerprints are utilized to characterize each compound. Forest graph embedded deep feed forward network (forgeNet) is proposed to train. The experimental results show that forgeNet performs better than support vector machines (SVM), random forest (RF), logical regression (LR), Naive Bayes (NB), XGBoost, LightGBM and gcForest. forgeNet could identify 19 compounds in Erhuang decoction (EhD) and Dexamethasone (DXMS) more accurately.
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Garber A, Barnard L, Pickrell C. Review of Whole Plant Extracts With Activity Against Herpes Simplex Viruses In Vitro and In Vivo. J Evid Based Integr Med 2021; 26:2515690X20978394. [PMID: 33593082 PMCID: PMC7894602 DOI: 10.1177/2515690x20978394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Herpes simplex viruses, HSV-1 and HSV-2, are highly contagious and cause lifelong, latent infections with recurrent outbreaks of oral and/or genital lesions. No cure exists for HSV-1 or HSV-2 infections, but antiviral medications are commonly used to prevent and treat outbreaks. Resistance to antivirals has begun to emerge, placing an importance on finding new and effective therapies for prophylaxis and treatment of HSV outbreaks. Botanicals may be effective HSV therapies as the constituents they contain act through a variety of mechanisms, potentially making the development of antiviral resistance more challenging. A wide variety of plants from different regions in the world have been studied for antiviral activity against HSV-1 and/or HSV-2 and showed efficacy of varying degrees. The purpose of this review is to summarize research conducted on whole plant extracts against HSV-1 and/or HSV-2 in vitro and in vivo. The majority of the research reviewed was conducted in vitro using animal cell lines, and some studies used an animal model design. Also summarized are a limited number of human trials conducted using botanical therapies on HSV lesions.
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Affiliation(s)
- Anna Garber
- Department of Research, Canadian College of Naturopathic Medicine, Toronto, Ontario, Canada
| | - Lianna Barnard
- Department of Research, Canadian College of Naturopathic Medicine, Toronto, Ontario, Canada
| | - Chris Pickrell
- Department of Research, Canadian College of Naturopathic Medicine, Toronto, Ontario, Canada
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Tong Y, Jing Y, Zhao D, Zhang L, Zeng S. Fluoroquinolone-resistant uncomplicated urinary tract infections, Chinese herbal medicine may provide help. AFRICAN JOURNAL OF TRADITIONAL, COMPLEMENTARY, AND ALTERNATIVE MEDICINES 2011; 8:108-14. [PMID: 22754063 DOI: 10.4314/ajtcam.v8i5s.18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We assessed the effects of Chinese herbs on the uncomplicated urinary tract infections (UTIs) in women caused by fluoroquinolone-resistant strains. A total of 56 pre-menopausal women with uncomplicated UTIs caused by fluoroquinolone-resistant strains were included. Urine cultures were carried out. All organisms were proved to be fluoroquinolone-resistant at baseline. The patients were orally administrated Chinese herbal concoction for ten days. Chinese herbal concoction eradicated the primary pathogen in 71.4% of the patients at the 1-week follow-up. Among the 20 patients who had bacteriologic failures in the Day 5 of treatment, 2 developed superinfection. Of the failures in the group, Proteus mirabilis, Staphylococcus epidermidis and Providencia rettgeri were implicated in 50.0%, 50.0% and 100.0% of the failures, respectively. The clinical outcomes were also good, with cure or improvement for more than 80% of all subjects. About 14% of the study subjects reported at least one potential adverse event. The adverse events most frequently reported were nausea and diarrhea. All patients tolerated the symptoms. The adverse reactions did not prevail after discontinuation of the medication. Chinese herbal therapy may be an acceptable alternative for the treatment of uncomplicated UTIs caused by fluoroquinolone-resistant uropathogens.
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Affiliation(s)
- Yanqing Tong
- Department of Nephrology, The First Affilliated Hospital to Changchun University of Chinese Medicine, Changchun city, Jilin province, China.
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Tong Y, Wu Q, Zhao D, Liu Y, Cao M, Zhang L, Zeng S. Effects of Chinese herbs on the hemagglutination and adhesion of Escherichia coli strain in vitro. AFRICAN JOURNAL OF TRADITIONAL, COMPLEMENTARY, AND ALTERNATIVE MEDICINES 2010; 8:82-7. [PMID: 22238488 DOI: 10.4314/ajtcam.v8i1.60530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of this study is to evaluate Chinese herbs' efficacy on adhesive properties of Escherichia coli (E. coli). The effects of Chinese herbal solution on the hemagglutination and adhesion by E. coli strain were studied. E. coli C16 was isolated from a patient with urinary tract infection. The MIC value of herbal solution for the E. coli C16 was 0.1g/ml. The MBC value was 0.2g/ml. The effects of herbal solution on the hemagglutination abilities of E. coli C16 were dependent on the herbal solution used. The strain C16 lost half of its hemagglutination abilities when the herbal solution concentration was at MIC (0.05g/ml). Herbal solution decreased the adherence of strain C16 in a dose-dependent way. The numbers of adherent bacteria were reduced to 45% of the control values after growth with herbal solution at MIC. The results show that anti-adhesion is one mode of action for Chinese herbs used against pathogens.
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Affiliation(s)
- YanQing Tong
- Department of Nephrology, The First Affilliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin province, China.
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Tong Y, Han B, Guo H, Liu Y. Protection of Chinese herbs against adenine-induced chronic renal failure in rats. AFRICAN JOURNAL OF TRADITIONAL, COMPLEMENTARY, AND ALTERNATIVE MEDICINES 2010; 7:331-8. [PMID: 21731165 DOI: 10.4314/ajtcam.v7i4.56701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of the study is to evaluate the efficacy of Chinese herbs (Angelica sinensis, Ligusticum wallichii, Salvia miltiorrhiza, Rhizoma dioscoreae, Rhodiola crenilata, Astragalus membranaceus and Angelica sinensis) on adenine-induced chronic renal failure in rats. 30 age-matched male Wistar rats were divided into three groups. Rats in group A (n = 10), B (n = 10) and C (n = 10) were fed a standard laboratory chow and allowed tap water ad libitum. In group B and C, renal failure was induced by the administration of a diet containing 0.75% adenine for 28 days which began at day 0. Rats in group C were given Chinese herbs (40 ml/kg with drug concentration 1.75 g/ml) beginning at day 0. Urine albumin, blood urea nitrogen (BUN) and creatinine were determined at days 0, 14 and 28. At day 28, the animals were killed and their kidneys removed for light microscope evaluation. Body weight in Group B decreased more significantly than that in Group C (p = 0.032) at day 28. The rats in group B demonstrated more severe proteinuria and higher Serum creatinine and BUN levels than group C at day 14 and day 28 (P < 0.05, 0.01). All rats given adenine developed marked structural renal damage involving the tubule and interstitium. The values were much less severe in group C than those in group B. In adenine-induced chronic renal failure rats, the protective effects of these Chinese herbs were of a significant nature. Our results do support the notion that these Chinese herbs are useful in deferring the advance of chronic renal failure. We recommend Chinese herbs as a beneficial treatment for pre-end stage chronic renal failure.
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Affiliation(s)
- Yanqing Tong
- Department of Nephrology, The First Affilliated Hospital to Changchun University of Chinese Medicine, Changchun city, Jilin province, China.
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Block KI, Mead MN. Immune system effects of echinacea, ginseng, and astragalus: a review. Integr Cancer Ther 2004; 2:247-67. [PMID: 15035888 DOI: 10.1177/1534735403256419] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Traditional herbal medicine provides several remedies for strengthening the body's resistance to illness through effects on immune system components. This review article examines 3 popular herbal immune stimulants that are often of interest to cancer patients. Echinacea, a native of North America, is widely used to prevent, or provide early treatment for, colds. Preclinical studies lend biological plausibility to the idea that echinacea works through immune mechanisms. Numerous clinical trials have been carried out on echinacea preparations: it appears that the extracts shorten the duration and severity of colds and other upper respiratory infections (URIs) when given as soon as symptoms become evident. However, trials of long-term use of echinacea as a preventive have not shown positive results. Ginseng has been studied in some depth as an antifatigue agent, but studies of immune mechanisms have not proceeded so far. Preclinical evidence shows some immune-stimulating activity. There have been several clinical trials in a variety of different diseases. Astragalus is the least-studied agent. There are some preclinical trials that show intriguing immune activity. The herbs discussed appear to have satisfactory safety profiles. Cancer patients may wish to use these botanicals to inhibit tumor growth or to boost resistance to infections. However, passive immunotherapy with herbs, with no mechanism to expose tumor antigens, is unlikely to be effective in inhibiting tumor growth. Although the margin of safety for these herbs is large, more research is needed to demonstrate the clear value of using herbs to improve resistance to infections.
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Affiliation(s)
- Keith I Block
- Institute for Integrative Cancer Care and Block Center for Integrative Cancer Care, Evanston, Illinois 60201, USA.
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Vermani K, Garg S. Herbal medicines for sexually transmitted diseases and AIDS. JOURNAL OF ETHNOPHARMACOLOGY 2002; 80:49-66. [PMID: 11891087 DOI: 10.1016/s0378-8741(02)00009-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sexually transmitted diseases (STDs) and acquired immunodeficiency syndrome (AIDS) are gaining significant importance at present due to rapid spread of the diseases, high cost of treatment, and the increased risk of transmission of other STDs and AIDS. Current therapies available for symptomatic treatment of STDs and AIDS are quite expensive beyond the reach of common man and are associated with emergence of drug resistance. Many patients of STDs and AIDS are seeking help from alternative systems of medicines such as Unani, Chinese, Ayurvedic, naturopathy, and homeopathy. Since a long time, medicinal plants have been used for the treatment of many infectious diseases without any scientific evidence. At present there is more emphasis on determining the scientific evidence and rationalization of the use of these preparations. Research is in progress to identify plants and their active principles possessing activity against sexually transmitted pathogens including human immunodeficiency virus (HIV) with an objective of providing an effective approach for prevention of transmission and treatment of these diseases. In the present review, plants reported to possess activity or used in traditional systems of medicine for prevention and treatment of STDs including AIDS, herbal formulations for vaginal application, and topical microbicides from herbal origin, have been discussed.
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Affiliation(s)
- Kavita Vermani
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, SAS Nagar, 160 062, Punjab, India
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Abstract
Herpes simplex virus (HSV) infection in the burn patient is thought to occur relatively frequently. Most commonly, children with significant burns, particularly involving the head and neck, are affected. Burn related immunosuppression is thought to allow reactivation of latent HSV in most cases, although primary HSV infection has been recognized. Clinical manifestations vary from asymptomatic viral shedding, to prolonged fever with eruption of vesicles, to rare cases of systemic visceral dissemination. Healing partial thickness wounds and donor sites are most prone to infection. Laboratory confirmation of HSV infection relies on direct demonstration of the virus and/or observation of a rise in antibody titer. Treatment of an established HSV infection includes use of IV Acyclovir, meticulous wound care, and efforts to prevent nosocomial spread. The vast majority of cases resolve without sequelae unless complicated by systemic, multiorgan HSV infection.
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Affiliation(s)
- S N McGill
- Department of Surgery, Queen's University, Kingston, Canada
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Kobayashi M, Mori K, Kobayashi H, Pollard RB, Suzuki F. The regulation of burn-associated infections with herpes simplex virus type 1 or Candida albicans by a non-toxic aconitine-hydrolysate, benzoylmesaconine. Part 1: Antiviral and anti-fungal activities in thermally injured mice. Immunol Cell Biol 1998; 76:202-8. [PMID: 9682963 DOI: 10.1046/j.1440-1711.1998.00735.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
As compared with normal unburned mice, thermally injured mice have been shown to be 50-100 times more susceptible to HSV type 1 (HSV-1) or Candida albicans infection. Benzoylmesaconine (BEN) improved the resistance of thermally injured mice against infection with HSV-1 or C. albicans to the level observed in normal mice. Mortality rates of normal mice exposed to lethal amounts of these pathogens were not affected by the BEN treatment, while significant survival effects were produced in these mice after treatment with acyclovir (against HSV-1) or amphotericin B (against C. albicans). Benzoylmesaconine did not inhibit the growth of these pathogens in vitro and did not directly reduce the viability of the pathogens. However, burned mice inoculated with CD4+ T cells from BEN-treated mice resisted infections from these pathogens. These results suggested that, through the generation of CD4+ T cells, BEN recovered the impaired resistance of thermally injured mice to infection by HSV-1 or C. albicans.
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Affiliation(s)
- M Kobayashi
- Department of Internal Medicine, University of Texas Medical Branch, Galveston 77555-0835, USA
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Nakajima N, Utsunomiya T, Kobayashi M, Herndon DN, Pollard RB, Suzuki F. In vitro induction of anti-type 2 T cells by glycyrrhizin. Burns 1996; 22:612-7. [PMID: 8982539 DOI: 10.1016/s0305-4179(96)00053-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycyrrhizin (GR), an active component of licorice roots, has been previously shown to induce the generation of anti-type 2 T cells (anti-BI2T cells), which are able to counteract the activity of burn-induced CD8+ type 2 T cells (BI2T cells), in thermally injured and normal mice. In the present study, anti-BI2T cells were generated in vitro in cultures of spleen cells stimulated with GR. Anti-BI2T cells were induced in vitro when splenic mononuclear cells (SMNC) were stimulated in vitro for 24 to 72 h with 0.1-10 micrograms/ml of GR. Anti-BI2T cell activity was detected when suppressor macrophages (M phi) were depleted from SMNC after stimulation with GR. However, the GR-stimulated generation of anti-BI2T cells required the participation of M phi or their sonicated fractions. Anti-BI2T cells induced in vitro by GR were identified as Vicia villosa lectin adherent IFN7 producing-CD4+ T cells lacking the ability to produce IL-2, IL-4 or IL-10. These results indicate that anti-BI2T cells are generated by GR in vitro. M phi are not only necessary for the generation of anti-BI2T cells induced by GR but also inhibit their activity.
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Affiliation(s)
- N Nakajima
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, USA
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Ikemoto K, Kobayashi M, Fukumoto T, Morimatsu M, Pollard RB, Suzuki F. 2-Carboxyethylgermanium sesquioxide, a synthetic organogermanium compound, as an inducer of contrasuppressor T cells. EXPERIENTIA 1996; 52:159-66. [PMID: 8608818 DOI: 10.1007/bf01923363] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
2-Carboxyethylgermanium sesquioxide (Ge-132), a synthesized organogermanium compound with immunomodulating activities, was shown to be an inducer of anti-suppressor T cells in normal mice. The suppressor cell activity of T6S cells, a clone of burn-induced CD8+ IL-4-producing suppressor T cells, was clearly inhibited when a mixed lymphocyte-tumor cell reaction of the clone was conducted with splenic mononuclear cells from mice treated orally with a 100 mg/kg dose of Ge-132. The activity of anit-suppressor cells was demonstrated in spleens of mice 2 days after treatment with Ge-132 and reached its peak on day 3. The anti-suppressor cells induced by the compound were of a contrasuppressor T cell-linage, because they were characterized as CD4+ CD28+ TCRalpha/beta+ Vicia villosa lectin-adherent T cells. These cells produced IFN-gamma but did not produce IL-2, IL-4, IL-6 or IL-10 in their culture fluids. CD4+ anti-suppressor T cells induced by Ge-132 may be different from other subsets of CD4+ T cells because Th1 and Th2 cells generated in our laboratory did not adhere to Vicia villosa lectin-coated petri dishes, and each produced specific cytokines. Th1 cells produced IFN-gamma and IL-2 while Th2 cells produce IL-4 and IL-10 in vitro. These results suggest that Ge-132 may be useful as an inducer of contrasuppressor T cells in immunocompromised individuals bearing suppressor T cells. To eliminate suppressor T cells from immunocompromised hosts may result in improved resistance from various opportunistic infections.
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Affiliation(s)
- K Ikemoto
- Department of Neurology, Yamaguchi University of Medical School, Japan
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