Synthesis of a tetralone derivative of ampicillin to control ampicillin-resistant Staphylococcusaureus.

Due to the rapid emergence of antibiotic resistant new bacterial strains and new infections, there is an urgent need for novel or newly modified and efficient alternatives of treatment. However, conventional antibiotics are still used in therapeutic settings but their efficacy is uncertain due to the rapid evolution of drug resistance. In the present study, we have synthesized a new derivative of conventional antibiotic ampicillin using SN2-type substitution reaction. NMR and mass analysis of the newly synthesized derivative of ampicillin confirmed it as ampicillin-bromo-methoxy-tetralone (ABMT). Importantly, ABMT is revealed to have efficient activity against Staphylococcus aureus (S. aureus) with a MIC value of 32 µg ml-1 while ampicillin was not effective, even at 64 µg ml-1 of concentration. Electron microscopy results confirmed the membrane-specific killing of S. aureus at 1 h of treatment. Additionally, molecular docking analysis revealed a strong binding affinity of ABMT with ß-lactamase via the formation of a closed compact bridge. Our findings, avail a new derivative of ampicillin that could be a potential alternative to fight ampicillin-resistant bacteria possibly by neutralizing the ß-lactamase action.

Correction: The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3'-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis.

[This corrects the article DOI: 10.1371/journal.pgen.1004749.].

Efficient delivery of methotrexate to MDA-MB-231 breast cancer cells by a pH-responsive ZnO nanocarrier.

Methotrexate (MTX), an efficient chemotherapy medication is used in treating various malignancies. However, the breast cancer cell line MDA-MB-231 has developed resistance to it due to low levels of the MTX transport protein, and reduced folate carrier (RFC), making it less effective against these cancer cells. Here we designed a very simple, biocompatible, and non-toxic amine-capped ZnO quantum dots to overcome the MTX resistance on the MDA-MB-231 breast cancer cell line. The QD was characterized by HRTEM, DLS EDX, FT-IR, UV-Vis, and Fluorescence spectroscopy. MTX loading onto the QD was confirmed through fluorescence and UV-Vis spectroscopy. Additionally, extensive confocal microscopic investigations were carried out to determine whether the MTX was successfully released on the MDA-MB-231 cell line. It was discovered that QD is a better pH-responsive delivery system than the previous ones because it successfully delivers MTX to the MDA-MB-231 at a higher rate on an acidic pH than it does at a physiological pH. QD also has anticancer activity and can eradicate cancer cells on its own. These factors make the QD to be an effective pH-responsive delivery system that can improve the efficacy of the medication in therapeutic diagnosis.

Gut-Antimicrobial Peptides: Synergistic Co-Evolution with Antibiotics to Combat Multi-Antibiotic Resistance.

Due to huge diversity and dynamic competition, the human gut microbiome produces a diverse array of antimicrobial peptides (AMPs) that play an important role in human health. The gut microbiome has an important role in maintaining gut homeostasis by the AMPs and by interacting with other human organs via established connections such as the gut-lung, and gut-brain axis. Additionally, gut AMPs play a synergistic role with other gut microbiota and antimicrobials to maintain gut homeostasis by fighting against multi-antibiotic resistance (MAR) bacteria. Further, conventional antibiotics intake creates a synergistic evolutionary pressure for gut AMPs, where antibiotics and gut AMPs fight synergistically against MAR. Overall, gut AMPs are evolving under a complex and highly synergistic co-evolutionary pressure created by the various interactions between gut microbiota, gut AMPs, and antibiotics; however, the complete mechanism is not well understood. The current review explores the synergistic action of gut AMPs and antibiotics along with possibilities to fight against MAR bacteria.

A subunit vaccine against pneumonia: targeting Streptococcus pneumoniae and Klebsiella pneumoniae.

Community-acquired pneumonia is primarily caused by Streptococcus pneumoniae and Klebsiella pneumoniae, two pathogens that have high morbidity and mortality rates. This is largely due to bacterial resistance development against current antibiotics and the lack of effective vaccines. The objective of this work was to develop an immunogenic multi-epitope subunit vaccine capable of eliciting a robust immune response against S. pneumoniae and K. pneumoniae. The targeted proteins were the pneumococcal surface proteins (PspA and PspC) and choline-binding protein (CbpA) of S. pneumoniae and the outer membrane proteins (OmpA and OmpW) of K. pneumoniae. Different computational approaches and various immune filters were employed for designing a vaccine. The immunogenicity and safety of the vaccine were evaluated by utilizing many physicochemical and antigenic profiles. To improve structural stability, disulfide engineering was applied to a portion of the vaccine structure with high mobility. Molecular docking was performed to examine the binding affinities and biological interactions at the atomic level between the vaccine and Toll-like receptors (TLR2 and 4). Further, the dynamic stabilities of the vaccine and TLRs complexes were investigated by molecular dynamics simulations. While the immune response induction capability of the vaccine was assessed by the immune simulation study. Vaccine translation and expression efficiency was determined through an in silico cloning experiment utilizing the pET28a(+) plasmid vector. The obtained results revealed that the designed vaccine is structurally stable and able to generate an effective immune response to combat pneumococcal infection. Supplementary Information: The online version contains supplementary material available at 10.1007/s13721-023-00416-3.

Surfactin-like lipopeptides from Bacillus clausii efficiently bind to spike glycoprotein of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) rapidly spread across the globe, infecting millions and causing hundreds of deaths. It has been now around three years but still, it remained a serious threat worldwide, even after the availability of some vaccines. Bio-surfactants are known to have antiviral activities and might be a potential alternative for the treatment of SARS-CoV-2 infection. In the present study, we have isolated and purified, a surfactin-like lipopeptide produced by a probiotic bacterial strain Bacillus clausii TS. Upon purification and characterization with MALDI analysis, the molecular weight of the lipopeptide is confirmed as 1037 Da (similar to surfactin C) which is known to have antiviral activities against various enveloped viruses. Purified surfactin-like lipopeptide showed efficient binding and inhibition of SARS-CoV-2 spike (S1) protein, revealed by competitive ELISA assay. Further, we have explored the complete thermodynamics of the inhibitory binding of surfactin-like lipopeptide with S1 protein using isothermal titration calorimetric (ITC) assay. ITC results are in agreement with ELISA with a binding constant of 1.78 × 10-4 M-1. For further validation of the inhibitory binding of surfactin-like lipopeptide with S1 protein and its receptor binding domain (RBD), we performed molecular docking, dynamics, and simulation experiments. Our results suggested that surfactin could be a promising drug agent for the spike protein targeting drug development strategy against SARS-CoV-2 and other emerging variants.Communicated by Ramaswamy H. Sarma.

Nitric oxide mediated hypoxia dynamics in COVID-19.

Several COVID-19 patients frequently experience with happy hypoxia. Sometimes, the level of nitric oxide (NO) in COVID-19 patients was found to be greater than in non-COVID-19 hypoxemics and most of the cases lower. Induced or inhaled NO has a long history of usage as a therapy for hypoxemia. Excessive production of ROS and oxidative stress lower the NO level and stimulates mitochondrial malfunction is the primary cause of hypoxia-mediated mortality in COVID-19. Higher level of NO in mitochondria also the cause of dysfunction, because, excess NO can also diffuse quickly into mitochondria or through mitochondrial nitric oxide synthase (NOS). A precise dose of NO may increase oxygenation while also acting as an effective inhibitor of cytokine storm. NOS inhibitors may be used in conjunction with iNO therapy to compensate for the patient's optimal NO level. NO play a key role in COVID-19 happy hypoxia and a crucial component in the COVID-19 pathogenesis that demands a reliable and easily accessible biomarker to monitor.

Preventing Respiratory Viral Diseases with Antimicrobial Peptide Master Regulators in the Lung Airway Habitat.

The vast surface area of the respiratory system acts as an initial site of contact for microbes and foreign particles. The whole respiratory epithelium is covered with a thin layer of the airway and alveolar secretions. Respiratory secretions contain host defense peptides (HDPs), such as defensins and cathelicidins, which are the best-studied antimicrobial components expressed in the respiratory tract. HDPs have an important role in the human body's initial line of defense against pathogenic microbes. Epithelial and immunological cells produce HDPs in the surface fluids of the lungs, which act as endogenous antibiotics in the respiratory tract. The production and action of these antimicrobial peptides (AMPs) are critical in the host's defense against respiratory infections. In this study, we have described all the HDPs secreted in the respiratory tract as well as how their expression is regulated during respiratory disorders. We focused on the transcriptional expression and regulation mechanisms of respiratory tract HDPs. Understanding how HDPs are controlled throughout infections might provide an alternative to relying on the host's innate immunity to combat respiratory viral infections.

Plant-Derived Antimicrobial Peptides: Novel Preservatives for the Food Industry.

Food spoilage is a widespread issue brought on by the undesired growth of microbes in food products. Thousands of tons of usable food or food products are wasted every day due to rotting in different parts of the world. Several food preservation techniques are employed to prevent food from rotting, including the use of natural or manufactured chemicals or substances; however, the issue persists. One strategy for halting food deterioration is the use of plant-derived antimicrobial peptides (AMPs), which have been investigated for possible bioactivities against a range of human, plant, and food pathogens. The food industry may be able to benefit from the development of synthetic AMPs, produced from plants that have higher bioactivity, better stability, and decreased cytotoxicity as a means of food preservation. In order to exploit plant-derived AMPs in various food preservation techniques, in this review, we also outline the difficulties in developing AMPs for use as commercial food preservatives. Nevertheless, as technology advances, it will soon be possible to fully explore the promise of plant-derived AMPs as food preservatives.

NOTCH signaling in COVID-19: a central hub controlling genes, proteins, and cells that mediate SARS-CoV-2 entry, the inflammatory response, and lung regeneration.

In the lungs of infected individuals, the downstream molecular signaling pathways induced by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are incompletely understood. Here, we describe and examine predictions of a model in which NOTCH may represent a central signaling axis in lung infection in Coronavirus Disease 2019 (COVID-19). A pathway involving NOTCH signaling, furin, ADAM17, and ACE2 may be capable of increasing SARS-CoV-2 viral entry and infection. NOTCH signaling can also upregulate IL-6 and pro-inflammatory mediators induced to hyperactivation in COVID-19. Furthermore, if NOTCH signaling fails to turn down properly and stays elevated, airway regeneration during lung healing can be inhibited-a process that may be at play in COVID-19. With specific NOTCH inhibitor drugs in development and clinical trials for other diseases being conducted, the roles of NOTCH in all of these processes central to both infection and healing merit contemplation if such drugs might be applied to COVID-19 patients.

Conservation and Enhanced Binding of SARS-CoV-2 Omicron Spike Protein to Coreceptor Neuropilin-1 Predicted by Docking Analysis.

The Omicron variant of SARS-CoV-2 bears peptide sequence alterations that correlate with a higher infectivity than was observed in the original SARS-CoV-2 isolated from Wuhan, China. We analyzed the CendR motif of spike protein and performed in silico molecular docking with neuropilin-1 (Nrp1), a receptor-ligand interaction known to support infection by the original variant. Our analysis predicts conserved and slightly increased energetic favorability of binding for Omicron CendR:Nrp1. We propose that the viral spike:Nrp1 coreceptor pathway may contribute to the infectivity of the Omicron variant of SARS-CoV-2.

Short Amphiphiles or Micelle Peptides May Help to Fight Against COVID-19.

BACKGROUND: COVID-19 is a global threat as a result of the incessant spread of SARS-CoV- 2, necessitating the rapid availability of effective antiviral medications to protect our society. For SARSCoV- 2, a group of peptides has already been indicated, although their effectiveness has yet to be shown. SARS-CoV-2 is an enveloped virus with hydrophobic fusion protein and spike glycoproteins. METHODS: Here, we have compiled a list of amphiphilic peptides that have been published, as well as their in-silico docking studies with the SARS-CoV-2 spike glycoprotein. RESULTS: The findings demonstrated that spike protein and amphiphilic peptides with increased binding affinity create a complex. It was also observed that PalL1 (ARLPRTMVHPKPAQP), 10AN1 (FWFTLIKTQAKQPARYRRFC), THETA defensin (RCICGRGICRLL), and mucroporin M1 (LFRLIKSLIKRLVSAFK) showed the binding free energy of more than -1000 kcal/mol. Molecular pI and hydrophobicity are also important factors of peptides to enhance the binding affinity with spike protein of SARS-CoV-2. CONCLUSION: In light of these findings, it is crucial to compare the in-vitro to in-vivo efficacy of amphiphilic peptides in order to produce an efficient anti-SARS-CoV-2 peptide therapy that might assist control the present pandemic scenario.

Facile and Green Fabrication of Highly Competent Surface-Modified Chlorogenic Acid Silver Nanoparticles: Characterization and Antioxidant and Cancer Chemopreventive Potential.

The eco-friendly, cost-effective, and green fabrication of nanoparticles is considered a promising area of nanotechnology. Here, we report on the green synthesis and characterization of bovine serum albumin (BSA)-decorated chlorogenic acid silver nanoparticles (AgNPs-CGA-BSA) and the studies undertaken to verify their plausible antioxidant and antineoplastic effects. High-resolution transmission electron microscopy (HR-TEM), dynamic light scattering, X-ray diffraction, and Fourier transform infrared analyses depict an average mean particle size of ∼96 nm, spherical morphology, and nanocrystalline structure of AgNPs-CGA-BSA. DPPH scavenging and inhibition of lipid peroxidation signify the noticeable in vitro antioxidant potential of the nanoparticles. The in vitro experimental results demonstrate that AgNPs-CGA-BSA shows significant cytotoxicity to Dalton's lymphoma ascites (DLA) cells and generates an enhanced intracellular reactive oxygen species and oxidized glutathione (GSSG) and reduced glutathione (GSH) in DLA cells. Furthermore, mechanism investigation divulges the pivotal role of the downregulated expression of superoxide dismutase (SOD) and catalase (CAT), and these ultimately lead to apoptotic chromatin condensation in AgNPs-CGA-BSA-treated DLA cells. In addition, in vivo experiments reveal an excellent decrease in tumor cell count, an increase in serum GSH and CAT, SOD, and glutathione peroxidase activities, and a decrease in the malondialdehyde (MDA) level in DLA-bearing mice after AgNPs-CGA-BSA treatment. These findings suggest that the newly synthesized biogenic green silver nanoparticles have remarkable in vitro antioxidant and antineoplastic efficacy that triggers cytotoxicity, oxidative stress, and chromatin condensation in DLA cells and in vivo anticancer efficacy that enhances the host antioxidant status, and these might open a new path in T-cell lymphoma therapy.

Characterization and Antimicrobial Studies of Iturin-Like and Bogorol-Like Lipopeptides From Brevibacillus spp. Strains GI9 and SKDU10.

Accession numbers for whole-genome sequence of Brevibacillus sp. strain GI9 and SKDU10 are CAGD01000001 to CAGD01000061 and LSSO00000000, respectively. Members of the genus Brevibacillus have been demonstrated to produce a variety of bioactive compounds including polyketides, lipopeptides and bacteriocins. Lipopeptides are non-ribosomally synthesized surface-active compounds with antimicrobial, antitumor, and immune-stimulatory activities. They usually exhibit strong antifungal and antibacterial activities and are considered as promising compounds in controlling fungal diseases. In this study, we have characterized two lipopeptides from Brevibacillus sp. strains GI9 and SKDU10. The corresponding lipopeptides were purified by reverse-phase high-performance liquid chromatography. Mass analysis and characterization by MALDI-TOF-MS (Matrix-assisted laser desorption ionization time-of-flight mass spectrometry) analysis revealed production of an iturin-like lipopeptide by strain GI9 and bogorol-like lipopeptide by strain SKDU10. Both lipopeptides exhibited broad spectrum antibacterial activity and inhibited the growth of various fungi. They showed minimum inhibitory concentration (MIC) values between 90 and 300 µg/ml against indicator strains of bacteria and drug-resistant Candida indicator strains. The lipopeptides did not show phytotoxic effect in seed germination experiments but caused hemolysis. Further, both lipopeptides inhibited the growth of fungi on fruits and vegetables in in vitro experiments, thereby exhibited potential use in biotechnological industry as effective biocontrol agents.

Biologia Futura: use of biocides during COVID-19-global reshuffling of the microbiota.

Aim The article reviews the current usage of biocides during this lockdown period for sanitizing our living areas due to the pandemic and discusses the pros and cons. Subject COVID-19 spread like wildfire to over 200 countries of the world across all continents. The causative agent, novel coronavirus (SARS-CoV-2) is being counter attacked by a thorough application of disinfectants and sterilants. However, the virus mutated over 30 times during this global pandemic, creating panic and leading to enhanced pathogenicity and consequently to more stringent sanitation measures for controlling it. However, excessive use of different types of biocides for disinfecting surfaces is highly alarming in several cases. Extensive application of biocides affects the microbial flora, leading to an abrupt decrease in the number and diversity of beneficial microbes that may directly affect the functioning of nutrient cycles. Results The increased concentration of biocides in agricultural land via surface water or pond water indirectly affect the soil and water ecosystem, soil aggregation and fertility. This will also lead to the flourishing of resistant strains due to loss of competition from the other species, which fail to persist after prolonged use of biocides. Conclusion It is necessary to realize the environmental impacts of biocides and sterilants. It is the right time to stop their entry into the agricultural ecosystem by following adequate management strategies and complete neutralization.

Characterization of Iturin V, a Novel Antimicrobial Lipopeptide from a Potential Probiotic Strain Lactobacillus sp. M31.

Members of lactic acid bacteria group are known to produce various antimicrobial substances. Cyclic lipopeptides are one such potent class of amphipathic natural biosurfactants that exhibit bactericidal and immunomodulatory properties. In this study, we aimed to investigate antimicrobial and immunomodulatory activities of a lipopeptide secreted by a LAB isolate strain M31 identified as a member of the genus Lactobacillus. The lipopeptide that was purified using a combination of chromatographic techniques and matrix-assisted laser desorption/ionization-time of flight of pure lipopeptide displayed a molecular weight of 1002 Da. MS/MS analysis confirmed the presence of 7 amino acids (Asp-Tyr-Asp-Val-Pro-Asp-Ser) and a C13 beta-hydroxy fatty acid. The amino acid composition assigned lipopeptide to iturin class. However, the replacement of Gln with Val revealed it to represent a novel iturin named as iturin V. Iturin V showed antibacterial activity and did not cause hemolysis or cytotoxicity upto 125 µg/mL. It induced secretion of pro-inflammatory cytokines TNF-alpha and IL-12 in murine dendritic cells. Probiotic features of strain M31 coupled with notable activity of iturin V against species of the genera Pseudomonas and Vibrio suggest that strain M31 has potential application for pathogen intervention treatments in processing of aquatic food products.

Identification of a novel proline-rich antimicrobial protein from the hemolymph of Antheraea mylitta.

Antimicrobial proteins (AMPs) are small, cationic proteins that exhibit activity against bacteria, viruses, parasites, fungi as well as boost host-specific innate immune responses. Insects produce these AMPs in the fat body and hemocytes, and release them into the hemolymph upon microbial infection. Hemolymph was collected from the bacterially immunized fifth instar larvae of tasar silkworm, Antheraea mylitta, and an AMP was purified by organic solvent extraction followed by size exclusion and reverse-phase high-pressure liquid chromatography. The purity of AMP was confirmed by thin-layer chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The molecular mass was determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry as 14 kDa, and hence designated as AmAMP14. Peptide mass fingerprinting of trypsin-digested AmAMP14 followed by de novo sequencing of one peptide fragment by tandem mass spectrometry analysis revealed the amino acid sequences as CTSPKQCLPPCK. No homology was found in the database search and indicates it as a novel AMP. The minimum inhibitory concentration of the purified AmAMP14 was determined against Escherichia coli, Staphylococcus aureus, and Candida albicans as 30, 60, and 30 µg/ml, respectively. Electron microscopic examination of the AmAMP14-treated cells revealed membrane damage and release of cytoplasmic contents. All these results suggest the production of a novel 14 kDa AMP in the hemolymph of A. mylitta to provide defense against microbial infection.

Successful Control of a Co-Infection Caused by Candida albicans and Pseudomonas aeruginosa in Keratitis.

INTRODUCTION: Nowadays, the co-infection of different classes of pathogens is a major concern. The objective of this study was to develop a successful therapy for keratitis caused by the co-infection of Candida sp. with Pseudomonas sp, which is difficult to cure. The study is based on a 47 years old male farmer showing redness and watering in the right eye for 15-days. ; Methods: The microbiological examination was performed to isolate the causative organisms, i.e. Pseudomonas aeruginosa and Candida albicans. They were cultured separately along with their co-culture and treated with ciprofloxacin and amphotericin B during the growing stage to predict a definite cure. ; Results: Scanning electron microscope (SEM) results confirmed the inter-specific interaction between the two different types of microorganisms. Amphotericin-B and Ciprofloxacin showed the least MIC value for both organisms in co-culture. ; Conclusion: Treatment with Amphotericin-B and 5% ciprofloxacin effectively hindered the growth of Pseudomonas aeruginosa and Candida albicans, the co-infection of which caused keratitis. This therapy may be successfully implied for such cases of co-infection in the future.

In Silico Identification of a Potent Arsenic Based Approved Drug Darinaparsin against SARS-CoV-2: Inhibitor of RNA Dependent RNA polymerase (RdRp) and Essential Proteases.

BACKGROUND: COVID-19 is a life-threatening novel corona viral infection to our civilization and spreading rapidly. Tremendousefforts have been made by the researchers to search for a drug to control SARS-CoV-2. METHODS: Here, a series of arsenical derivatives were optimized and analyzed with in silico study to search the inhibitor of RNA dependent RNA polymerase (RdRp), the major replication factor of SARS-CoV-2. All the optimized derivatives were blindly docked with RdRp of SARS-CoV-2 using iGEMDOCK v2.1. RESULTS: Based on the lower idock score in the catalytic pocket of RdRp, darinaparsin (-82.52 kcal/- mol) was revealed to be the most effective among them. Darinaparsin strongly binds with both Nsp9 replicase protein (-8.77 kcal/mol) and Nsp15 endoribonuclease (-8.3 kcal/mol) of SARS-- CoV-2 as confirmed from the AutoDock analysis. During infection, the ssRNA of SARS-CoV-2 is translated into large polyproteins forming viral replication complex by specific proteases like 3CL protease and papain protease. This is also another target to control the virus infection where darinaparsin also performs the inhibitory role to proteases of 3CL protease (-7.69 kcal/mol) and papain protease (-8.43 kcal/mol). CONCLUSION: In the host cell, the furin protease serves as a gateway to the viral entry and darinaparsin docked with furin protease, which revealed a strong binding affinity. Thus, screening of potential arsenic drugs would help in providing the fast in-vitro to in-vivo analysis towards the development of therapeutics against SARS-CoV-2.

LPD-12: a promising lipopeptide to control COVID-19.

INTRODUCTION: The recent pandemic outbreak of SARS-CoV-2 has been associated with a lethal atypical pneumonia, making COVID-19 an urgent public health issue with an increasing rate of mortality and morbidity. There are currently no vaccines or therapeutics available for COVID-19, which is causing an urgent search for a new drug to combat the COVID-19 pandemic. The lipid membrane alternation efficiency of small antimicrobial lipopeptides enables them to block viral membrane fusion to the host cell. Lipopeptides could serve as potential antiviral agents, by interacting or competing with viral fusion proteins. METHODS: This study screened seven different lipopeptides (tsushimycin, daptomycin, surfactin, bacillomycin, iturin, srfTE, and LPD-12) and docked them individually against the spike (S)-glycoprotein of SARS-CoV-2. RESULTS: Based on the maximum docked score and minimum atomic contact energy, LPD-12 (-1137.38 kcal) was the appropriate molecule for proper binding with the S-glycoprotein of SARS-CoV-2 and thus significantly interrupted its affinity of binding with angiotensin-converting enzyme-2 (ACE2), which is the only receptor molecule found to be facilitating disease development. The results confirmed a strong binding affinity of LPD-12 with ACE2, with a binding free energy of -1621.62 kcal, which could also reciprocally prevent the binding of S-protein. CONCLUSTION: It can be concluded that LPD-12 may act as a potential therapeutic drug, by reducing the entry of SARS-CoV-2 to the human cells via the ACE2 receptor and related infections.