Abstract SARS-CoV-2, a novel pathogenic human coronavirus, emerged in December of 2019 in Wuhan (Hubei province, China). In most cases, the infection causes a mild to moderate respiratory illness. ...However, a undefined group of infected may develop a severe or critical illness: Coronavirus disease 2019 (COVID-19) with acute respiratory distress syndrome (ARDS) and many other complications. Current efforts are focused on limiting the spread of the virus in the population. COVID-19 treatments are intensively evaluated, however, 8 months since the start of the pandemic and despite hundreds of clinical trials, our knowledge of effective treatments is still poor. In this review, we present the current status of drugs and treatments used during SARS-CoV-2 infection. Host-directed and virus-directed drugs, as well as new compounds specific for SARS-CoV-2 are presented. 1. Introduction. 2. Host-directed drugs. 2.1. Antiparasitic drugs with potential for repurposing. 2.2. Host proteases inhibitors. 2.3. Endocytosis inhibitors. 2.4. Immunomodulating drugs affecting host. 3. Virus-directed drugs. 3.1. Broad-range-antiviral drugs. 3.2. Inhibitors of viral S glycoprotein. 3.3. New potential virus-directed drugs against SARS-CoV-2. 4. Conclusions
Abstract In 2019, a new human pandemic coronavirus (SARS-CoV-2) emerged in Wuhan, China. We present the knowledge about SARS-CoV-2 compared to SARS-CoV and MERS-CoV. The SARS-CoV-2 is similar to ...other coronaviruses, nevertheless, differences were observed. Cell entry of SARS-CoV-2 is facilitated by cleavage of spike protein by furin. The receptor-binding motif of SARS-CoV-2 spike protein forms a larger binding interface and more contacts with host receptor ACE2 compared those of in SARS-CoV. Unlike other coronaviruses, the SARS-CoV-2 spike protein has a motif, known to bind integrins. Nucleocapsid protein and RNA-dependent RNA polymerase of SARS-CoV-2 display some structural differences compared to those of SARS-CoV as well. These features may increase the efficiency of the spread of SARS-CoV-2 and indicate the putative targets for specific antiviral therapy. 1. Taxonomy of Coronaviridae . 2. Structure of Betacoronavirus virion. 3. Genome of Betacoronavirus . 4. Proteins of Betacoronavirus . 5. Betacoronavirus replication cycle. 6. Pathogenesis of SARS-CoV-2. 6.1. Tissue and cellular pathogenesis. 6.2. Molecular basis of pathogenesis. 6.3. Immunopathological changes in COVID-19. 7. Conclusions
Outer membrane vesicles (OMVs) are bilayer structures released by bacteria for various purposes, e.g., response to environmental factors, bacterial communication, and interactions with host cells. ...One of the environmental variables bacteria need to react is the amount and availability of iron, a crucial element for bacteria biology. We have investigated the impact of the iron amount and availability on OMV secretion by pathogenic Neisseria gonorrhoeae, which, depending on the infection site, challenges different iron availability. N. gonorrhoeae releases OMVs in iron starvation and repletion growth environments. However, OMVs differed in physicochemical features and proteome according to iron amount and availability during the bacteria growth, as was analyzed by Liquid Chromatography-Tandem Mass Spectrometry, Infrared spectroscopy with a Fourier transform infrared spectrometer, and Atomic Force Microscopy. OMVs from iron starvation and repletion conditions had a higher variation in size, different flexibility, and different membrane protein and lipid components than OMVs isolated from control growth conditions. These OMVs also varied qualitatively and quantitatively in their total proteome composition and contained proteins unique for iron starvation and repletion conditions. Thus, the modulation of OMVs' properties seems to be a part of N. gonorrhoeae adaptation to surroundings and indicates a new direction of antigonococcal proceeding.
Bacteriophages are the most numerous entities on earth and are found everywhere their bacterial hosts live. As natural bacteria killers, phages are extensively investigated as a potential cure for ...bacterial infections. Neisseria gonorrhoeae (the gonococcus) is the etiologic agent of a sexually transmitted disease: gonorrhea. The rapid increase of resistance of N. gonorrhoeae to antibiotics urges scientists to look for alternative treatments to combat gonococcal infections. Phage therapy has not been tested as an anti-gonococcal therapy so far. To date, no lytic phage has been discovered against N. gonorrhoeae. Nevertheless, gonococcal genomes contain both dsDNA and ssDNA prophages, and viral particle induction has been documented. In this review, we consider literature data about the attempts of hunting for a bacteriophage specific for gonococci - the gonophage. We also discuss the potential application of prophage elements in the fight against N. gonorrhoeae. Temperate phages may be useful in preventing and treating gonorrhea as a scaffold for anti-gonococcal vaccine development and as a source of lytic enzymes with anti-gonococcal activity.
Bacteria of the
genus are Gram-negative diplococci including both pathogenic and commensal species. We focused on pathogenic
and commensal
. We have demonstrated that not only
, but also
induce the ...secretion of pro-inflammatory cytokines IL-6, TNF-α, and chemokines CXCL8 and CCL20 by infected epithelial cells. However,
triggers a lesser effect than does
. Furthermore,
and
invoke distinct effects on the expression of genes (JUNB, FOSB, NFKB1, NFKBIA) encoding protein components of AP-1 and NF-κB transcription factors. We have also shown that the infection of epithelial cells by
leads to significant overexpression of the long non-coding RNAs (lncRNAs), including MALAT1, ERICD, and RP11-510N19.5. This effect was not identified for
In conclusion, data on the expression of lncRNAs and cytokine secretion in response to
spp. exposure indicate new directions for research on
-host interactions and can provide further insights into virulence of not only pathogenic, but also commensal
spp.
The surface-enhanced Raman scattering (SERS) has been widely tested for its usefulness in microbiological studies, providing many information-rich spectra which are a kind of ‘whole-organism ...fingerprint’ and enabling identification of bacterial species. Here we show, previously not considered, the comprehensive SERS-chemometric analysis of five bacterial pathogens, namely Neisseria gonorrhoeae, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Haemophilus ducreyi, all being responsible for sexually transmitted diseases (STDs). In the designed biosensor, the direct, intrinsic format of the spectroscopic analysis was adopted for the SERS-based screening of gonorrhea and chlamydiosis due to vibrational analysis of men's urethra swabs. Our experiments demonstrated that the applied method enables identification the individual species of the Neisseria genus with high accuracy. In order to differentiate the sexually transmitted pathogens and to classify the clinical samples of male urethra swabs, three multivariate methods were used. In the external validation the created models correctly classified the men's urethra swabs with prediction accuracy reaching 89% for SIMCA and 100% for PLS-DA. As a result, the developed protocol enables: (i) simple and non-invasive analysis of clinical samples (the collection of urethra swabs specimens could be carried out at different points of care, such as doctor's office); (ii) fast analysis (<15 min); (iii) culture-free identification; (iv) sensitive and reliable SERS-based diagnosis of STD. The simplicity of the developed detection procedure, supported by high sensitivity, reproducibility, and specificity, open a new path in the improvement of the point-of-care applications.
•The SERS-chemometric differentiation of pathogens responsible for the sexually transmitted diseases.•Sensitive, direct, and non-invasive SERS-based screening of gonorrhea and chlamydiosis screening.•Rapid (< 15 min) and culture and growth-free method.•The possibility to identify bacteria at genus and species level.
Surface-enhanced Raman spectroscopy (SERS) is a research method in which a lack of cost-effective, versatile platforms with high enhancement factor (EF) is still a major obstacle to its widespread ...use. The platforms should be also easy to manufacture, stable in time (for weeks or even for months) and manufactured with a highly reproducible method.
We demonstrate SERS platforms based on silicon modified on the surface by laser ablation and covered with SERS-active metal. The substrates were fabricated by a femtosecond laser, thus the method is simple, very fast and creates highly uniform SERS platforms in a large number. The platform was tested with para-mercaptobenzoic acid (p-MBA) in terms of sensitivity and reproducibility. The calculated EF was at the level of 108 and the standard deviation (SD) gives 7% for 10−6 M solution of p-MBA based on the intensity of the band at 1073 cm−1. Optimized SERS substrate also exhibits excellent stability for up to six months.
We also give the proof-of-concept of using our platform and, for the first time, the SERS analysis of the most important human opportunistic fungal pathogen Candida spp. (Candida glabrata, Candida albicans SN148 and C. albicans BWP17). Finally, the chemometric analysis in the form of Principal Component Analysis (PCA) allowed to strain differentiation of Candida spp., and to distinguish the studied Candida species from Gram-positive bacterial samples with Staphylococcus aureus. Our results demonstrate that the proposed SERS platform is a perfect substrate for detection, identification and differentiation between fungal and bacterial pathogens using SERS technique.
The functioning of DNA repair systems is based on correct interactions between proteins involved in DNA repair. Very Short Patch (VSP) repair is a DNA repair system that corrects mismatches resulting ...from the deamination of 5-methylcytosine. The key enzyme in the VSP system is Vsr endonuclease, which can cleave mismatched DNA independently of accessory proteins. Until now, in vivo activity has only been shown for V.EcoKDcm - the only Vsr endonuclease in Escherichia coli. Additionally, the VSP system of E. coli is the only one for which interactions between proteins of the system have been demonstrated. Neisseria gonorrhoeae FA1090 is the first bacterium that we previously demonstrated to encode two active in vitro Vsr endonucleases: V.NgoAXIII and V.NgoAXIV.
We elucidate the mutator phenotype of N. gonorrhoeae mutants with disrupted genes encoding V.NgoAXIII or V.NgoAXIV endonuclease. Furthermore, we investigate the interactions between gonococcal Vsr endonucleases and MutL and MutS proteins. The Vsr endonucleases physically interact with gonococcal MutL protein but not with MutS protein. In the presence of the MutL protein, the efficiency of DNA cleavage by both V.NgoAXIII and V.NgoAXIV endonucleases increases, resulting in a decrease in the amount of Vsr enzyme required to complete digestion of mismatched DNA. Both Vsr endonucleases are also stimulated in vitro by the MutL protein of E. coli. In turn, the gonococcal MutS protein hinders DNA cleavage by the Vsr endonucleases. However, this effect is overridden in the presence of MutL, and furthermore, the simultaneous presence of MutL and MutS causes an increase in the efficiency of DNA cleavage by the Vsr endonucleases compared to the reaction catalyzed by V.NgoAXIII or V.NgoAXIV alone.
For the first time, interactions between proteins of the DNA repair system encoded by N. gonorrhoeae that are responsible for the correction of mismatches resulting from the 5-methylcytosine deamination were identified. The increase in activity of Vsr endonucleases in the presence of MutL protein could allow for reduced synthesis of the Vsr endonucleases in cells, and the susceptibility of gonococcal Vsr endonucleases on MutL protein of E. coli implies a universal mechanism of Vsr stimulation by MutL protein.
HP1 is a temperate bacteriophage, belonging to the
family and infecting
Rd. By in silico analysis and molecular cloning, we characterized
and
gene products, present in the previously proposed lytic ...module of HP1 phage. The amino acid sequence of the
gene product revealed the presence of signal-arrest-release (SAR) and muraminidase domains, characteristic for some endolysins. HP1 endolysin was able to induce lysis on its own when cloned and expressed in
, but the new phage release from infected
cells was suppressed by inhibition of the secretion (
) pathway. Protein encoded by
gene is a transmembrane protein, with unusual C-out and N-in topology, when overexpressed/activated. Its overexpression in
did not allow the formation of large pores (lack of leakage of β-galactosidase), but caused cell death (decrease in viable cell count) without lysis (turbidity remained constant). These data suggest that
gene encodes a SAR-endolysin and that the
gene product is a pinholin. HP1 SAR-endolysin is responsible for cell lysis and HP1 pinholin seems to regulate the cell lysis and the phage progeny release from
cells, as new phage release from the natural host was inhibited by deletion of the
gene.
The accurate identification of microorganisms belonging to vaginal microflora is crucial for establishing which microorganisms are responsible for microbial shifting from beneficial symbiotic to ...pathogenic bacteria and understanding pathogenesis leading to vaginosis and vaginal infections. In this study, we involved the surface-enhanced Raman spectroscopy (SERS) technique to compile the spectral signatures of the most significant microorganisms being part of the natural vaginal microbiota and some vaginal pathogens. Obtained data will supply our still developing spectral SERS database of microorganisms. The SERS results were assisted by Partial Least Squares Regression (PLSR), which visually discloses some dependencies between spectral images and hence their biochemical compositions of the outer structure. In our work, we focused on the most common and typical of the reproductive system microorganisms (Lactobacillus spp. and Bifidobacterium spp.) and vaginal pathogens: bacteria (e.g., Gardnerella vaginalis, Prevotella bivia, Atopobium vaginae), fungi (e.g., Candida albicans, Candida glabrata), and protozoa (Trichomonas vaginalis). The obtained results proved that each microorganism has its unique spectral fingerprint that differentiates it from the rest. Moreover, the discrimination was obtained at a high level of explained information by subsequent factors, e.g., in the inter-species distinction of Candida spp. the first three factors explain 98% of the variance in block Y with 95% of data within the X matrix, while in differentiation between Lactobacillus spp. and Bifidobacterium spp. (natural flora) and pathogen (e.g., Candida glabrata) the information is explained at the level of 45% of the Y matrix with 94% of original data. PLSR gave us insight into discriminating variables based on which the marker bands representing specific compounds in the outer structure of microorganisms were found: for Lactobacillus spp. 1400 cm−1, for fungi 905 and 1209 cm−1, and for protozoa 805, 890, 1062, 1185, 1300, 1555, and 1610 cm−1. Then, they can be used as significant marker bands in the analysis of clinical subjects, e.g., vaginal swabs.
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