Erythromycin derivatives inhibit HIV-1 replication in macrophages through modulation of MAPK activity to induce small isoforms of C/EBPbeta

Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations

MOTIVATION

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe-drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe-drug associations.

RESULTS

In this article, we proposed a novel method, Graph2MDA, to predict microbe-drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe-drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaning of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75-95% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method.

AVAILABILITY AND IMPLEMENTATION

Source codes and preprocessed data are available at https://github.com/moen-hyb/Graph2MDA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Effects of Erythromycin on the Proliferation and Apoptosis of Cultured Nasal Polyp-Derived Cells and the Extracellular Signal-Regulated Kinase (ERK)/Mitogen-Activated Protein Kinase (MAPK) Signaling Pathway

Background

Erythromycin and its derivatives have been used to treat nasal polyposis and reduce inflammation, but the mechanism of action remains unclear. The extracellular signal-regulated kinase (ERK) and mitogen-activated protein kinase (MAPK) pathway proteins are expressed in nasal polyps. The aim of this study was to investigate the effects of erythromycin on cell proliferation, apoptosis, and the expression of p-MEK1 and p-ERK1 on cultured nasal polyp-derived cells.

Material/Methods

Nasal polyp-derived cells (n=32) and control cells from normal inferior turbinate tissue (n=32) were divided into four groups: the control group; the erythromycin-treated (100 μM) group; the selumetinib-treated (2 nM) group; and the erythromycin + selumetinib-treated group. Western blot was used to detect p-MEK1 and p-ERK1 proteins. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect mRNA expression of BCL-2 and BAX. Flow cytometry detected expression of Ki-67 and cell apoptosis. Cell apoptosis was evaluated by terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL). Spectrophotometry assessed caspase-3 activity.

Results

The expression of Ki-67 was significantly increased, and cell apoptosis was significantly reduced in untreated nasal polyp-derived cells compared with controls. Erythromycin treatment significantly decreased cell proliferation and the expression of p-MEK1 and p-ERK1, and increased apoptosis in nasal polyp-derived cells compared with control cells. Selumetinib treatment had a synergistic effect with erythromycin to reduce the expression of p-MEK1 and p-ERK1, reduce cell proliferation, and increase cell apoptosis.

Conclusions

In cultured cells derived from nasal polyps, erythromycin treatment reduced cell proliferation and increased apoptosis by inhibiting the activation of the ERK/MAPK signaling pathway.

Non-antibiotic 12-membered macrolides: design, synthesis and biological evaluation in a cigarette-smoking model

The 14-membered macrolide erythromycin A expresses three distinct biological properties, including antibacterial activity, gastrointestinal motor-stimulating activity and anti-inflammatory and/or immunomodulatory effects. Although low-dose, long-term therapy using 14- and 15-membered macrolides displaying anti-inflammatory and/or immunomodulatory activity effectively treats diffuse panbronchiolitis and chronic sinusitis, bacterial resistance may emerge. To address this issue, we developed the 12-membered non-antibiotic macrolide (8R,9S)-8,9-dihydro-6,9-epoxy-8,9-anhydropseudoerythromycin A (EM900) that promotes monocyte to macrophage differentiation, a marker for anti-inflammatory and/or immunomodulatory effects, without possessing antibacterial activity. In this article, we report that the new macrolide derivative (8R,9S) -de(3'-N-methyl)-3'-N-(p-chlorobenzyl)-de(3-O-cladinosyl)-3-dehydro-8,9-dihydro-6,9-epoxy-8,9-anhydropseudoerythromycin A 12,13-carbonate (EM939) exhibited stronger promotive activity for monocyte to macrophage differentiation than that of the parent compound EM900 in addition to reduced cytotoxicity toward THP-1 cells and antibacterial inactivity. In a cigarette-smoking model used to simulate chronic obstructive pulmonary disease (COPD), the EM900 derivatives significantly attenuated lung and alveolar inflations, functionally and histologically, via oral administration. Because of these marked therapeutic effects, non-antibiotic EM900 derivatives may become central to the treatment of chronic inflammatory diseases such as COPD.

Altered PKR Signalling and C / EBPβ Expression is Associated with HLA-B27 Expression in Monocytic Cells

Infection caused by certain gram-negative bacteria, e.g. Salmonella, can trigger inflammatory joint disease reactive arthritis (ReA). It is suggested that the disease-triggering bacteria or bacterial components persist in patients for an abnormally long time. Development of ReA is strongly associated with tissue antigen HLA-B27. Previously, we reported an enhanced replication of Salmonella enteritidis and altered p38 MAP kinase signalling in HLA-B27-expressing monocytic cells. Here we aimed to investigate the role of HLA-B27 in regulation of double-stranded RNA-activated kinase (PKR)-related signalling in Salmonella-infected or Salmonella lipopolysaccharide (LPS)-stimulated human U937 monocytic cells, as PKR has been reported to modify p38 signalling in Salmonella-infected cells. In cells expressing HLA-B27, PKR is overexpressed and hypophosphorylated, and the expression of transcription factor CCAAT enhancer binding protein beta (C/EBPβ) is increased upon Salmonella infection and LPS stimulation. The expression of C/EBPβ is PKR-dependent in LPS-stimulated mock cells, whereas in LPS-stimulated B27 cells the majority of C/EBPβ is expressed in a PKR-independent manner. Our results show that the expression of HLA-B27 disturbs the PKR-mediated signalling pathway. Moreover, altered signalling is related to misfolding-linked Glu45 in the B pocket of the HLA-B27 heavy chain. We suggest that the expression of HLA-B27 HCs modulates the intracellular environment of monocyte/macrophages and the mechanisms that are important in eliminating intracellular S. enteritidis by altering the intracellular signalling. This phenomenon is at least partly dependent on the misfolding feature of the B27 molecule. These observations offer a novel mechanism by which HLA-B27 may modulate inflammatory response induced by ReA-triggering bacteria.

HIV-1 reprograms the migration of macrophages

Macrophages are motile leukocytes, targeted by HIV-1, thought to play a critical role in host dissemination of the virus. However, whether infection impacts their migration capacity remains unknown. We show that 2-dimensional migration and the 3-dimensional (3D) amoeboid migration mode of HIV-1-infected human monocyte-derived macrophages were inhibited, whereas the 3D mesenchymal migration was enhanced. The viral protein Nef was necessary and sufficient for all HIV-1-mediated effects on migration. In Nef transgenic mice, tissue infiltration of macrophages was increased in a tumor model and in several tissues at steady state, suggesting a dominant role for mesenchymal migration in vivo. The mesenchymal motility involves matrix proteolysis and podosomes, cell structures constitutive of monocyte-derived cells. Focusing on the mechanisms used by HIV-1 Nef to control the mesenchymal migration, we show that the stability, size, and proteolytic function of podosomes are increased via the phagocyte-specific kinase Hck and Wiskott-Aldrich syndrome protein (WASP), 2 major regulators of podosomes. In conclusion, HIV-1 reprograms macrophage migration, which likely explains macrophage accumulation in several patient tissues, which is a key step for virus spreading and pathogenesis. Moreover, Nef points out podosomes and the Hck/WASP signaling pathway as good candidates to control tissue infiltration of macrophages, a detrimental phenomenon in several diseases.

HIV-1 infection of T cells and macrophages are differentially modulated by virion-associated Hck: a Nef-dependent phenomenon

The proline repeat motif (PxxP) of Nef is required for interaction with the SH3 domains of macrophage-specific Src kinase Hck. However, the implication of this interaction for viral replication and infectivity in macrophages and T lymphocytes remains unclear. Experiments in HIV-1 infected macrophages confirmed the presence of a Nef:Hck complex which was dependent on the Nef proline repeat motif. The proline repeat motif of Nef also enhanced both HIV-1 infection and replication in macrophages, and was required for incorporation of Hck into viral particles. Unexpectedly, wild-type Hck inhibited infection of macrophages, but Hck was shown to enhance infection of primary T lymphocytes. These results indicate that the interaction between Nef and Hck is important for Nef-dependent modulation of viral infectivity. Hck-dependent enhancement of HIV-1 infection of T cells suggests that Nef-Hck interaction may contribute to the spread of HIV-1 infection from macrophages to T cells by modulating events in the producer cell, virion and target cell.

Immunomodulatory effects of antimicrobial agents. Part I: antibacterial and antiviral agents

Despite impressive therapeutic progresses in the battle against infections, microorganisms are still a threat to mankind. With hundreds of antibacterial molecules, major concerns remain about the emergence of resistant and multidrug-resistant pathogens. On the other hand, the antiviral drug armamentarium is comprised of only a few dozens of compounds which are highly pathogen specific, and resistance is also a concern. According to Arturo Casadevall (Albert Einstein College of Medicine, NY, USA), we have now entered the third era of anti-infective strategy, which intends to favor the interplay between active molecules and the immune system. The first part of this review focuses on the potential immunomodulating properties of anti-infective agents, beginning with antibacterial and antiviral agents.

Unexpected applications of secondary metabolites

Secondary metabolites have been found to have interesting applications over and above their well-known medical uses, e.g., as antimicrobials, etc. These alternative applications include antitumor, cholesterol-lowering, immunosuppressant, antiprotozoal, antihelminth, antiviral and anti-ageing activities. Polyene antibiotics, such as amphotericin B, are of use as antiprion agents, antitumor drugs and against leishmaniasis. Other microbial natural products that show antibiotic activity are used against cancer e.g., doxorubicin, neomycin, β-lactams, bleomycin and rapamycin. Macrolide antibiotics, such as erythromycin, clarithromycin and azithromycin, improve pulmonary function in patients suffering from panbioncholitis. Pigments like prodigiosin and shikonin have antitumor activity, while violacein has anti-ulcer and antitumor activity and also acts as an antiprotozoal agent. Statins, in addition to lowering cholesterol and LDL levels, also decrease elevated C-reactive protein (CRP) levels independent of their cholesterol effects. Immunosuppressants have many alternative effects: (i) Cyclosporin is proving useful in treatment of inflammatory disease such as asthma and muscular dystrophy. (ii) Rapamycin is extremely useful in preventing restenosis of stents grafted in balloon angioplasty. (iii) Tacrolimus and ascomycin help in treating inflammatory skin disease such as allergic contact dermatitis and psoriasis. Artemisinin, an antimalarial agent, is also showing antitumor activity. Other natural products, including those from plants (betulinic acid and shikonin), animals (bryostatins) and microbes (squalestatin and sophorolipids) have a multiplicity of potentially useful actions. Unexpected functions of known secondary metabolites are continuously being unraveled, and are fulfilling some of the needs of present day medicine and show great promise for the future.

Host hindrance to HIV-1 replication in monocytes and macrophages

Monocytes and macrophages are targets of HIV-1 infection and play critical roles in multiple aspects of viral pathogenesis. HIV-1 can replicate in blood monocytes, although only a minor proportion of circulating monocytes harbor viral DNA. Resident macrophages in tissues can be infected and function as viral reservoirs. However, their susceptibility to infection, and their capacity to actively replicate the virus, varies greatly depending on the tissue localization and cytokine environment. The susceptibility of monocytes to HIV-1 infection in vitro depends on their differentiation status. Monocytes are refractory to infection and become permissive upon differentiation into macrophages. In addition, the capacity of monocyte-derived macrophages to sustain viral replication varies between individuals. Host determinants regulate HIV-1 replication in monocytes and macrophages, limiting several steps of the viral life-cycle, from viral entry to virus release. Some host factors responsible for HIV-1 restriction are shared with T lymphocytes, but several anti-viral mechanisms are specific to either monocytes or macrophages. Whilst a number of these mechanisms have been identified in monocytes or in monocyte-derived macrophages in vitro, some of them have also been implicated in the regulation of HIV-1 infection in vivo, in particular in the brain and the lung where macrophages are the main cell type infected by HIV-1. This review focuses on cellular factors that have been reported to interfere with HIV-1 infection in monocytes and macrophages, and examines the evidences supporting their role in vivo, highlighting unique aspects of HIV-1 restriction in these two cell types.

CCAAT/enhancer-binding proteins and the pathogenesis of retrovirus infection

Previous studies indicate that two upstream CCAAT/enhancer-binding protein (C/EBP) sites and C/EBPbeta are required for subtype B HIV-1 gene expression in cells of the monocyte-macrophage lineage. The mechanisms of C/EBP regulation of HIV-1 transcription and replication remain unclear. This review focuses on studies concerning the role of C/EBP factors in HIV-1, human T-cell leukemia virus type 1, and SIV transcription in various cell types and tissues cultured in vitro, animal models and during human infection. The structure and function of the C/EBPbeta gene and the related protein isoforms are discussed along with the transcription factors, coactivators, viral proteins, cytokines and chemokines that affect C/EBP function.

Erythronolides H and I, new erythromycin congeners from a new halophilic actinomycete Actinopolyspora sp. YIM90600

Erythronolides H and I, novel congeners of the clinically important antibacterial drug erythromycin A, have been isolated from the new halophilic actinomycete Actinopolyspora sp. YIM90600. In addition to producing the new erythromycin congeners, A. sp. YIM90600 produces erythromycin C in a high titer. The presence of the C-14 hydroxyl moiety and the C-6/C-18-epoxide in erythronolide H and the spiroketal moiety of erythronolide I sheds new insights into structural diversity of erythromycin analog libraries potentially accessible by combinatorial biosynthesis.