Molecular dynamic analyses of the interaction of SARS-CoV-1 or 2 variants with various angiotensin-converting enzyme-2 species.

The transmembrane glycoprotein angiotensin-converting enzyme 2 (ACE2) is a key component of the renin-angiotensin system (RAS). It was shown to be the receptor of severe acute respiratory syndrome coronavirus 2 in the COVID-19 outbreak (SARS-COV-2). Furthermore, ACE2 aids in the transport of amino acids across the membrane. ACE2 is lost from the membrane, resulting in soluble ACE2 (sACE2). We aim to examine the structural conformation alterations between SARS-CoV-1 or 2 variants at various periods with ACE2 from various sources, particularly in the area where it interacts with the viral protein and the receptor. It is important to study the molecular dynamics of ACE2/SARS-COV RBD when the structure is available on the database. Here we analyzed the crystal structure of ACE2 from Human, Dog, Mus, Cat, and Bat ACE2 in complex with RBD from SARS-COV-1 and SARS-COV-2. The result shows, there is a variation in the type of residues, number of contact atoms and hydrogen bonds in ACE2 and RBD during the interaction interfaces. By using molecular dynamics simulation, we can measure RMSD, RMSF, SASA, Rg and the difference in the percentage of α helix and ß strand. As bat ACE2 & SARS-CoV-2 RBD found to have a high amount of ß strand compared to another structure complex, while hACE2 & SARS-CoV-1 RBD has fewer amounts of ß strand. Our study provides a deep view of the structure which is available and a summary of many works around ACE2/SARS-CoV RBD interaction.Communicated by Ramaswamy H. Sarma.

Review green synthesis of silver nanoparticles by using plant extracts and their antimicrobial activity.

Interest in the biosynthesis of nanoparticles has increased in the last era by researchers. Nanoparticles have several applications in different fields like optoelectronics, magnetic devices, drug delivery, and sensors. Nanoparticle synthesis by green methods is safe for the environment and should be explored and encouraged popularly since various plants' have the high extent to form these nanoparticles. Worldwide, UV spectroscopy, X-ray diffraction, Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Dynamic Light Scattering (DLS), Atomic Force Microscopy (AFM) besides Fourier Transform Infrared Spectroscopy (FTIR) are used in many ways for characterize nanoparticles. The most advantageous use of AgNPs is their great attribution to be used as antimicrobial agents. Finally, concept of AgNPs synthesis is deserved to be the modern technical and medical concern. The current review shows a complete comprehensive and analytical survey of the biosynthesis of AgNPs with a particular focus on their activities as antimicrobials and the possible theories of their effect on the microbial cell and all influenced secondary metabolites.

In-silico screening of Acacia pennata and Bridelia retusa reveals pinocembrin-7-O-ß-D-glucopyranoside as a promising ß-lactamase inhibitor to combat antibiotic resistance.

The ß-lactamase of Pseudomonas aeruginosa is known to degrade ß-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems. With the discovery of an extended-spectrum ß-lactamase in a clinical isolate of P. aeruginosa, the bacterium has become multi-drug resistant. In this study, we aim to identify new ß-lactamase inhibitors by virtually screening a total of 43 phytocompounds from two Indian medicinal plants. In the molecular docking studies, pinocembrin-7-O-ß-D-glucopyranoside (P7G) (-9.6 kcal/mol) from Acacia pennata and ellagic acid (EA) (-9.2 kcal/mol) from Bridelia retusa had lower binding energy than moxalactam (-8.4 kcal/mol). P7G and EA formed 5 (Ser62, Asn125, Asn163, Thr209, and Ser230) and 4 (Lys65, Ser123, Asn125, and Glu159) conventional hydrogens bonds with the active site residues. 100 ns MD simulations revealed that moxalactam and P7G (but not EA) were able to form a stable complex. The binding free energy calculations further revealed that P7G (-59.6526 kcal/mol) formed the most stable complex with ß-lactamase when compared to moxalactam (-46.5669 kcal/mol) and EA (-28.4505 kcal/mol). The HOMO-LUMO and other DFT parameters support the stability and chemical reactivity of P7G at the active site of ß-lactamase. P7G passed all the toxicity tests and bioavailability tests indicating that it possesses drug-likeness. Among the studied compounds, we identified P7G of A. pennata as the most promising phytocompound to combat antibiotic resistance by potentially inhibiting the ß-lactamase of P. aeruginosa.Communicated by Ramaswamy H. Sarma.

Molecular dynamic and bioinformatic studies of metformin-induced ACE2 phosphorylation in the presence of different SARS-CoV-2 S protein mutations.

The SARS-CoV-2 infection activates host kinases and causes high phosphorylation in both the host and the virus. There were around 70 phosphorylation sites found in SARS-CoV-2 viral proteins. Besides, almost 15,000 host phosphorylation sites were found in SARS-CoV-2-infected cells. COVID-19 is thought to enter cells via the well-known receptor Angiotensin-Converting Enzyme 2 (ACE2) and the serine protease TMPRSS2. Substantially, the COVID-19 infection doesn't induce phosphorylation of the ACE2 receptor at Serin-680(s680). Metformin's numerous pleiotropic properties and extensive use in medicine including COVID-19, have inspired experts to call it the "aspirin of the twenty-first century". Metformin's impact on COVID-19 has been verified in clinical investigations via ACE2 receptor phosphorylation at s680. In the infection of COVID-19, sodium-dependent transporters including the major neutral amino acid (B0AT1) is regulated by ACE2. The structure of B0AT1 complexing with the COVID-19 receptor ACE2 enabled significant progress in the creation of mRNA vaccines. We aimed to study the impact of the interaction of the phosphorylation form of ACE2-s680 with wild-type (WT) and different mutations of SARS-CoV-2 infection such as delta, omicron, and gamma (γ) on their entrance of host cells as well as the regulation of B0AT1by the SARS-CoV-2 receptor ACE2. Interestingly, compared to WT SARS-CoV-2, ACE2 receptor phosphorylation at s680 produces conformational alterations in all types of SARS-CoV-2. Furthermore, our results showed for the first time that this phosphorylation significantly influences ACE2 sites K625, K676, and R678, which are key mediators for ACE2-B0AT1 complex.

Antibacterial and Cytotoxic Effects of Biosynthesized Zinc Oxide and Titanium Dioxide Nanoparticles.

Nanotechnology is a rapidly developing field of research that studies materials having dimensions of less than 100 nanometers. It is applicable in many areas of life sciences and medicine including skin care and personal hygiene, as these materials are the essential components of various cosmetics and sunscreens. The aim of the present study was to synthesize Zinc oxide (ZnO) and Titanium dioxide (TiO2) nanoparticles (NPs) by using Calotropis procera (C. procera) leaf extract. Green synthesized NPs were characterized by UV spectroscopy, Fourier transform infrared (FTIR), X-ray diffraction (XRD), and Scanning Electron Microscopy (SEM) to investigate their structure, size, and physical properties. The antibacterial and synergistic effects of ZnO and TiO2 NPs along with antibiotics were also observed against bacterial isolates. The antioxidant activity of synthesized NPs was analyzed by their α-diphenyl-ß-picrylhydrazyl (DPPH) radical scavenging activity. In vivo toxic effects of the synthesized NPs were evaluated in albino mice at different doses (100, 200, and 300 mg/kg body weight) of ZnO and TiO2 NPs administered orally for 7, 14, and 21 days. The antibacterial results showed that the zone of inhibition (ZOI) was increased in a concentration-dependent manner. Among the bacterial strains, Staphylococcus aureus showed the highest ZOI, i.e., 17 and 14 mm against ZnO and TiO2 NPs, respectively, while Escherichia coli showed the lowest ZOI, i.e., 12 and 10 mm, respectively. Therefore, ZnO NPs are potent antibacterial agents compared to TiO2 NPs. Both NPs showed synergistic effects with antibiotics (ciprofloxacin and imipenem). Moreover, the DPPH activity showed that ZnO and TiO2 NPs have significantly (p > 0.05) higher antioxidant activity, i.e., 53% and 58.7%, respectively, which indicated that TiO2 has good antioxidant potential compared to ZnO NPs. However, the histological changes after exposure to different doses of ZnO and TiO2 NPs showed toxicity-related changes in the structure of the kidney compared to the control group. The current study provided valuable information about the antibacterial, antioxidant, and toxicity impacts of green synthesized ZnO and TiO2 NPs, which can be influential in the further study of their eco-toxicological effects.

HPLC Analysis and Molecular Docking Study of Myoporum serratum Seeds Extract with Its Bioactivity against Pathogenic Microorganisms and Cancer Cell Lines.

Natural constituents have been utilized to avoid humanity from various diseases, such as microbial infection and cancer, over several decades due to bioactive compounds. Myoporum serratum seeds extract (MSSE) was formulated via HPLC for flavonoid and phenolic analysis. Moreover, antimicrobial via well diffusion method, antioxidant via 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method, anticancer activities against HepG-2 cells (human hepatocellular cancer cell line), and MCF-7 cells (human breast cancer cell line), and molecular docking of the main detected flavonoid and phenolic compounds with the cancer cells were performed. The phenolic acids, including cinnamic acid (12.75 µg/mL), salicylic acid (7.14 µg/mL), and ferulic (0.97 µg/mL), while luteolin represents the main detected flavonoid with a concentration of 10.74 µg/mL, followed by apegenin 8.87 µg/mL were identified in MSSE. Staphylococcus aureus, Bacillus subtilis, Proteus vulgaris, and Candida albicans were inhibited by MSSE with 24.33, 26.33, 20.67, and 18.33 mm of inhibition zone, respectively. MSSE exhibited a low inhibition zone of 12.67 mm against Escherichia coli while showing no inhibitory activity against Aspergillus fumigatus. The values of MIC ranged from 26.58 to 136.33 µg/mL for all tested microorganisms. MBC/MIC index and cidal properties were attributed to MSSE for all tested microorganisms except E. coli. MSSE demonstrated anti-biofilm 81.25 and 50.45% of S. aureus and E. coli, respectively. IC50 of the antioxidant activity of MSSE was 120.11 µg/mL. HepG-2 and MCF-7 cell proliferation were inhibited with IC50 140.77 ± 3.86 µg/mL and 184.04 µg/mL, respectively. Via Molecular docking study, luteolin and cinnamic acid have inhibitory action against HepG-2 and MCF-7 cells, supporting the tremendous anticancer of MSSE.

Antibiotic-resistant bacteria in hospital wastewater treatment plant effluent and the possible consequences of its reuse in agricultural irrigation.

Wastewater from hospitals should be monitored precisely and treated properly before discharge and reuse to avoid epidemic and pandemic complications, as it contains hazardous pollutants for the ecosystem. Antibiotic residues in treated hospital wastewater effluents constitute a major environmental concern since they resist various wastewater treatment processes. The emergence and spread of multi-drug-resistant bacteria, that cause public health problems, are therefore always a major concern. The aims and objectives of this study were mainly to characterize the chemical and microbial properties of the hospital effluent of wastewater treatment plant (WWTP) before discharge to the environment. Special attention was paid to the presence of multiple resistant bacteria and the effects of hospital effluent reuse in irrigation on zucchini as an economically important plant. The risk of cell-free DNA carrying antibiotic resistance genes contained in the hospital effluent as a long-lasting hazard had been discussed. In this study, 21 bacterial strains were isolated from the effluent of a hospital WWTP. Isolated bacteria were evaluated for multi-drug resistance ability against 5 antibiotics (Tetracycline, Ampicillin, Amoxicillin, Chloramphenicol, and Erythromycin) at a concentration of 25 ppm. Out of them, three isolates (AH-03, AH-07, and AH-13) were selected because they recorded the highest growth in presence of tested antibiotics. Selected isolates were identified using 16S rRNA gene sequence homology as Staphylococcus haemolyticus (AH-03), Enterococcus faecalis (AH-07), and Escherichia coli (AH-13). Their susceptibility to ascending concentrations of tested antibiotics indicated that they were all susceptible at a concentration above 50 ppm. Results of the greenhouse experiment regarding the effect of hospital WWTP effluent reuse on zucchini plant fresh weights compared to that irrigated with fresh water indicated that the former recorded a limited increase in total fresh weights (6.2 g and 5.3 g/plant, respectively). Our results demonstrated the low impact of the reuse of Hospital WWTP effluent in agriculture irrigation compared to its greater risk in transferring multiple antibiotic bacteria and antibiotic resistance genes to soil bacteria through natural transformation.

Molecular Dynamic Analysis of Carbapenem-Resistant Klebsiella pneumonia's Porin Proteins with Beta Lactam Antibiotics and Zinc Oxide Nanoparticles.

To prevent the rapidly increasing prevalence of bacterial resistance, it is crucial to discover new antibacterial agents. The emergence of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae has been associated with a higher mortality rate in gulf union countries and worldwide. Compared to physical and chemical approaches, green zinc oxide nanoparticle (ZnO-NP) synthesis is thought to be significantly safer and more ecofriendly. The present study used molecular dynamics (MD) to examine how ZnO-NPs interact with porin protein (GLO21), a target of ß-lactam antibiotics, and then tested this interaction in vitro by determining the zone of inhibition (IZ), minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC), as well as the alteration of KPC's cell surface. The nanoparticles produced were characterized by UV-Vis spectroscopy, zetasizer, Fourier-transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). In silico investigation was conducted using a variety of computational techniques, including Autodock Vina for protein and ligand docking and Desmond for MD simulation. The candidate ligands that interact with the GLO21 protein were biosynthesized ZnO-NPs, meropenem, imipenem, and cefepime. Analysis of MD revealed that the ZnO-NPs had the highest log P value (-9.1 kcal/mol), which indicates higher permeability through the bacterial surface, followed by cefepime (-7.9 kcal/mol), meropenem (-7.5 kcal/mol), and imipenem (-6.4 kcal/mol). All tested compounds and ZnO-NPs possess similar binding sites of porin proteins. An MD simulation study showed a stable system for ZnO-NPs and cefepime, as confirmed by RMSD and RMSF values during 100 ns trajectories. The test compounds were further inspected for their intersection with porin in terms of hydrophobic, hydrogen, and ionic levels. In addition, the stability of these bonds were measured by observing the protein-ligand contact within 100 ns trajectories. ZnO-NPs showed promising results for fighting KPC, represented in MIC (0.2 mg/mL), MBC (0.5 mg/mL), and ZI (24 mm diameter). To draw the conclusion that ZnO-NP is a potent antibacterial agent and in order to identify potent antibacterial drugs that do not harm human cells, further in vivo studies are required.

Antibiofilm Potential of Coelomic Fluid and Paste of Earthworm Pheretima posthuma (Clitellata, Megascolecidae) against Pathogenic Bacteria.

Antibiotic drug resistance is a global public health issue that demands new and novel therapeutic molecules. To develop new agents, animal secretions or products are used as an alternative agent to overcome this problem. In this study, earthworm (Pheretima posthuma) coelomic fluid (PCF), and body paste (PBP) were used to analyze their effects as antibiofilm agents against four bacterial isolates MH1 (Pseudomonas aeruginosa MT448672), MH2 (Escherichia coli MT448673), MH3 (Staphylococcus aureus MT448675), and MH4 (Klebsiella pneumoniae MT448676). Coelomic fluid extraction and body paste formation were followed by minimum inhibitory concentrations (MICs), biofilm formation time kinetics, and an antibiofilm assay, using heat and cold shock, sunlight exposure auto-digestion, and test tube methods. The results showed that the MIC values of PCF and PBP against S. aureus, P. aeruginosa, K. pneumoniae, and E. coli bacterial isolates ranged from 50 to 100 µg/mL, while, the results related to biofilm formation for P. aeruginosa, S. aureus, and K. pneumoniae strains were observed to be highly significantly increased (p < 0.005) after 72 h. E. coli produced a significant (p < 0.004) amount of biofilm after 48 h. Following time kinetics, the antibiofilm activity of PCF and PBP was tested at different concentrations (i.e., 25-200 µg/mL) against the aforementioned four strains (MH1-MH4). The findings of this study revealed that both PBP (5.61 ± 1.0%) and PCF (5.23 ± 1.5%) at the lowest concentration (25 µg/mL) showed non-significant (p > 0.05) antibiofilm activity against all the selected strains (MH1-MH4). At 50 µg/mL concentration, both PCF and PBP showed significant (p < 0.05) biofilm inhibition (<40%) for all isolates. Further, the biofilm inhibitory potential was also found to be more significant (p < 0.01) at 100 µg/mL of PCF and PBP, while it showed highly significant (p < 0.001) biofilm inhibition at 150 and 200 µg/mL concentrations. Moreover, more than 90% biofilm inhibition was observed at 200 µg/mL of PCF, while in the case of the PBP, <96% biofilm reduction (i.e., 100%) was also observed by all selected strains at 200 µg/mL. In conclusion, earthworm body fluid and paste have biologically active components that inhibit biofilm formation by various pathogenic bacterial strains. For future investigations, there is a need for further study to explore the potential bioactive components and investigate in depth their molecular mechanisms from a pharmaceutical perspective for effective clinical utilization.

Fusarium oxysporum and Colletotrichum musae Associated with Wilt Disease of Coffea arabica in Coffee Gardens in Saudi Arabia.

This study aimed to identify if Fusarium and Colletotrichum species are linked to coffee leaf wilt symptoms (Coffea arabica L.) gardens in Jazan region, Kingdom Saudi Arabia. The symptomatic wilted leaves and shoots were collected from Jazan Mountain Region Development Authority (JMRDA) farm in jabal Fifa. Samples of roots and leaves tissues were plated on Dox' Agar medium and incubated for one week at 24oC. Two morphologically different fungus colonies grew on the medium. A PCR-based method was used for the molecular amplification and characterization of the fungi using a 18SrRNA specific primer. 1323 and 1501 bp PCR products were obtained by using the 1% agarose gel electrophoresis. The sequence analysis and genbank homology revealed that the present fungi were Fusarium oxysporum and Colletotrichum musae with 99 and 98% similarity, respectively. Both fungi sequences were submitted to the genebank under accession numbers OP010081 and OP010082, respectively. This is the first report of these two genera of fungi infecting the roots and leaves of coffee trees in Jazan Region of Saudi Arabia and suggests that other fungus species may play a significant role as diseases in other coffee-producing areas.