Antiviral peptides inhibiting the main protease of SARS-CoV-2 investigated by computational screening and in vitro protease assay

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in viral replication and transcription and received great attention as a vital target for drug/peptide development. Therapeutic agents such as small-molecule drugs or peptides that interact with the Cys-His present in the catalytic site of Mpro are an efficient way to inhibit the protease. Although several emergency-approved vaccines showed good efficacy and drastically dropped the infection rate, evolving variants are still infecting and killing millions of people globally. While a small-molecule drug (Paxlovid) received emergency approval, small-molecule drugs have low target specificity and higher toxicity. Besides small-molecule drugs, peptide therapeutics are thus gaining increasing popularity as they are easy to synthesize and highly selective and have limited side effects. In this study, we investigated the therapeutic value of 67 peptides targeting Mpro using molecular docking. Subsequently, molecular dynamics (MD) simulations were implemented on eight protein-peptide complexes to obtain molecular-level information on the interaction between these peptides and the Mpro active site, which revealed that temporin L, indolicidin, and lymphocytic choriomeningitis virus (LCMV) GP1 are the best candidates in terms of stability, interaction, and structural compactness. These peptides were synthesized using the solid-phase peptide synthesis protocol, purified by reversed-phase high-performance liquid chromatography (RP-HPLC), and authenticated by mass spectrometry (MS). The in vitro fluorometric Mpro activity assay was used to validate the computational results, where temporin L and indolicidin were observed to be very active against SARS-CoV-2 Mpro with IC50 values of 38.80 and 87.23 μM, respectively. A liquid chromatography-MS (LC-MS) assay was developed, and the IC50 value of temporin L was measured at 23.8 μM. The solution-state nuclear magnetic resonance (NMR) structure of temporin L was determined in the absence of sodium dodecyl sulfate (SDS) micelles and was compared to previous temporin structures. This combined investigation provides critical insights and assists us to further develop peptide inhibitors of SARS-CoV-2 Mpro through structural guided investigation.

Pathway-Controlled Aqueous Supramolecular Polymerization via Solvent-Dependent Chain Conformation Effects

Solute-solvent interactions play a critical role in multiple fields, including biology, materials science, and (physical) organic, polymer, and supramolecular chemistry. Within the growing field of supramolecular polymer science, these interactions have been recognized as an important driving force for (entropically driven) intermolecular association, particularly in aqueous media. However, to date, solute-solvent effects remain poorly understood in the context of complex self-assembly energy landscapes and pathway complexity. Herein, we unravel the role of solute-solvent interactions in controlling chain conformation effects, allowing energy landscape modulation and pathway selection in aqueous supramolecular polymerization. To this end, we have designed a series of oligo(phenylene ethynylene) (OPE)-based bolaamphiphilic Pt(II) complexes OPE2-4 bearing solubilizing triethylene glycol (TEG) chains of equal length on both molecule ends, but a different size of the hydrophobic aromatic scaffold. Strikingly, detailed self-assembly studies in aqueous media disclose a different tendency of the TEG chains to fold back and enwrap the hydrophobic molecular component depending on both the size of the core and the volume fraction of the co-solvent (THF). The relatively small hydrophobic component of OPE2 can be readily shielded by the TEG chains, leading to only one aggregation pathway. In contrast, the decreased capability of the TEG chains to effectively shield larger hydrophobic cores (OPE3 and OPE4) enables different types of solvent quality-dependent conformations (extended, partly back-folded and back-folded), which in turn induce various controllable aggregation pathways with distinct morphologies and mechanisms. Our results shed light on previously underappreciated solvent-dependent chain conformation effects and their role in governing pathway complexity in aqueous media.

Biodegradable and Dual-Responsive Polypeptide-Shelled Cyclodextrin-Containers for Intracellular Delivery of Membrane-Impermeable Cargo

The transport of membrane impermeable compounds into cells is a prerequisite for the efficient cellular delivery of hydrophilic and amphiphilic compounds and drugs. Transport into the cell's cytosolic compartment should ideally be controllable and it should involve biologically compatible and degradable vehicles. Addressing these challenges, nanocontainers based on cyclodextrin amphiphiles that are stabilized by a biodegradable peptide shell are developed and their potential to deliver fluorescently labeled cargo into human cells is analyzed. Host-guest mediated self-assembly of a thiol-containing short peptide or a cystamine-cross-linked polypeptide shell on cyclodextrin vesicles produce short peptide-shelled (SPSVss ) or polypeptide-shelled vesicles (PPSVss ), respectively, with redox-responsive and biodegradable features. Whereas SPSVss are permeable and less stable, PPSVss effectively encapsulate cargo and show a strictly regulated release of membrane impermeable cargo triggered by either reducing conditions or peptidase treatment. Live cell experiments reveal that the novel PPSVSS are readily internalized by primary human endothelial cells (human umbilical vein endothelial cells) and cervical cancer cells and that the reductive microenvironment of the cells' endosomes trigger release of the hydrophilic cargo into the cytosol. Thus, PPSVSS represent a highly efficient, biodegradable, and tunable system for overcoming the plasma membrane as a natural barrier for membrane-impermeable cargo.

Phospho-regulated Bim1/EB1 interactions trigger Dam1c ring assembly at the budding yeast outer kinetochore

Kinetochores form the link between chromosomes and microtubules of the mitotic spindle. The heterodecameric Dam1 complex (Dam1c) is a major component of the Saccharomyces cerevisiae outer kinetochore, assembling into 3 MDa‐sized microtubule‐embracing rings, but how ring assembly is specifically initiated in vivo remains to be understood. Here, we describe a molecular pathway that provides local control of ring assembly during the establishment of sister kinetochore bi‐orientation. We show that Dam1c and the general microtubule plus end‐associated protein (+TIP) Bim1/EB1 form a stable complex depending on a conserved motif in the Duo1 subunit of Dam1c. EM analyses reveal that Bim1 crosslinks protrusion domains of adjacent Dam1c heterodecamers and promotes the formation of oligomers with defined curvature. Disruption of the Dam1c‐Bim1 interaction impairs kinetochore localization of Dam1c in metaphase and delays mitosis. Phosphorylation promotes Dam1c‐Bim1 binding by relieving an intramolecular inhibition of the Dam1 C‐terminus. In addition, Bim1 recruits Bik1/CLIP‐170 to Dam1c and induces formation of full rings even in the absence of microtubules. Our data help to explain how new kinetochore end‐on attachments are formed during the process of attachment error correction.

A one-generation reproductive toxicity study of the mycotoxin ochratoxin A in Fischer rats

Ochratoxin A (OTA) is a mycotoxin produced by Aspergillus and Penicillium molds. Grain-based foods account for most human dietary exposures to OTA. OTA is a teratogen, but its reproductive and developmental effects are poorly understood. A one-generation reproductive toxicity study was conducted with groups of 16 male and 16 female Fischer rats exposed to 0, 0.026, 0.064, 0.16, 0.4 or 1.0 mg OTA/kg in diet. Dams exposed to 1.0 mg OTA/kg diet had statistically significant F1 pup losses between implantation and postnatal day (PND 4). Delays in preputial separation (PPS) and vaginal opening (VO) were indicative of delayed puberty in F1 rats. Mild renal lesions in nursing pups indicated that exposure prior to weaning impacted the kidneys. The developing kidney was more susceptible to OTA than the adult kidney. Significant increases in multi-oocyte follicles (MOFs) and proportional changes in resting and growing follicles were observed in F1 female ovaries. Plasma testosterone was reduced in F0 males, and there were negative effects on sperm quality in F0 and F1 male rats. The results confirm that continuous dietary exposure to OTA causes post-implantation fetotoxicity in dams, and renal and reproductive toxicity in their male and female offspring.

Simulated management effects on ammonia emissions from field applied manure

A need exists to improve the utilization of manure nutrients by minimizing NH(3) emissions from land application of manure. Management strategies to reduce NH(3) emissions are available; however, few have been validated under Canadian conditions. A well tested and accurate simulation model, however, can help overcome this challenge by determining appropriate management strategies for a given set of field conditions. The Volt'Air simulation model was utilized to estimate NH(3) volatilization from manure spreading for various manure spreading considerations under a range of atmospheric conditions typically encountered in eastern Canada. Considerations included: (i) soil liming, (ii) time of day of manure spreading, (iii) rainfall (timing and amount) and (iv) manure incorporation (timing, depth and manure coverage). Results demonstrated that liming to increase soil pH, increased NH(3) emissions by 3.3 kg ha(-1) for each increment of 0.1 pH (up to a 1.5 total increase), over no liming at 34.6 kg ha(-1). For each hour delay in manure spreading past 0800 h, NH(3) losses were reduced by 1.5 kg ha(-1). Rainfall (10mm) at least 20 h after manure application reduced losses, with increased reductions at higher rainfall amounts. Incorporation soon (1h) after application was best for NH(3) mitigation. Increasing the depth of incorporation by 5c m reduced NH(3) emissions by 4.4 kg ha(-1); also increasing manure coverage by incorporation reduced losses by 2 kg ha(-1) for each 10% increase in coverage, compared to surface application at 34.6 kg ha(-1). This investigation using Volt'Air yielded valuable information about simulating manure management strategies and the magnitude of their effects on NH(3) emissions.

Co-injection strategies to modify radiation sensitivity and tumor initiation in transgenic Zebrafish

The zebrafish has emerged as a powerful genetic model of cancer, but has been limited by the use of stable transgenic approaches to induce disease. Here, a co-injection strategy is described that capitalizes on both the numbers of embryos that can be microinjected and the ability of transgenes to segregate together and exert synergistic effects in forming tumors. Using this mosaic transgenic approach, gene pathways involved in tumor initiation and radiation sensitivity have been identified.

Medium- versus long-chain triglycerides for 27 days increases fat oxidation and energy expenditure without resulting in changes in body composition in overweight women

OBJECTIVE

To determine the effects of long-term consumption of medium chain (MCT) versus long chain triglycerides (LCT) on energy expenditure (EE), substrate oxidation and body composition.

HYPOTHESIS

MCT consumption will not result in greater EE, substrate oxidation, and body weight loss compared with LCT consumption.

RESEARCH METHODS AND PROCEDURES

Seventeen healthy obese women participated in this randomized, crossover inpatient trial. Meals were prepared and consumed on site for two periods of 27 days. Diets containing 40% of energy as fat, with treatment fat comprising 75% of the total fat, were designed to supply each subject with their individual weight-maintaining energy needs. The MCT diet contained 67% of treatment fat as MCT oil (49% octanoate, 50% decanoate) whereas the LCT diet contained exclusively beef tallow as treatment fat. Body composition was assessed by magnetic resonance imaging (MRI) on day 1 and 28 of each phase while energy expenditure was measured on day 2 and 27.

RESULTS

Changes in total and subcutaneous adipose tissue volumes following consumption of MCT and LCT were not different (-0.61+/-0.38 l vs -0.54+/-0.48 l and -0.58+/-0.35 l vs -0.48+/-0.40 l, respectively). Average EE and fat oxidation were greater (P<0.05) during MCT than LCT consumption (0.95+/-0.019 vs 0.90+/-0.024 kcal/min, respectively, for EE and 0.080+/-0.0026 vs 0.075+/-0.0022 g/min, respectively for fat oxidation).

DISCUSSION

These results show that long-term consumption of MCT enhances EE and fat oxidation in obese women, when compared to LCT consumption. The difference in body composition change between MCT and LCT consumption, although not statistically different, was consistent with differences predicted by the shifts in EE. It can be concluded that substitution of MCT for LCT in a targeted energy balance diet may prevent long-term weight gain via increased EE.

Specialized membrane domains for water transport in glial cells: high-resolution immunogold cytochemistry of aquaporin-4 in rat brain

Membrane water transport is critically involved in brain volume homeostasis and in the pathogenesis of brain edema. The cDNA encoding aquaporin-4 (AQP4) water channel protein was recently isolated from rat brain. We used immunocytochemistry and high-resolution immunogold electron microscopy to identify the cells and membrane domains that mediate water flux through AQP4. The AQP4 protein is abundant in glial cells bordering the subarachnoidal space, ventricles, and blood vessels. AQP4 is also abundant in osmosensory areas, including the supraoptic nucleus and subfornical organ. Immunogold analysis demonstrated that AQP4 is restricted to glial membranes and to subpopulations of ependymal cells. AQP4 is particularly strongly expressed in glial membranes that are in direct contact with capillaries and pia. The highly polarized AQP4 expression indicates that these cells are equipped with specific membrane domains that are specialized for water transport, thereby mediating the flow of water between glial cells and the cavities filled with CSF and the intravascular space.

An investigation of the mechanisms of action of 5-hydroxytryptamine in the suppression of ethanol intake

The effect of blockage of 5-hydroxytryptamine and norepinephrine uptake on voluntary ethanol consumption in rats was investigated. It was demonstrated that attenuation of ethanol intake occurred only as a result of treatment with specific 5-hydroxytryptamine uptake inhibitors. These results suggested that increasing the availability of central 5-hydroxytryptamine may in some way interfere with the positive reinforcing properties of ethanol. The second phase was designed to determine whether the attenuation of ethanol intake following blockade of 5-hydroxytryptamine uptake may be due to increased post-synaptic activity. Ethanol-preferring animals were pretreated with methergoline, a post-synaptic receptor blocker, followed by treatment with zimelidine, a 5-hydroxytryptamine uptake inhibitor. The results indicate that treatment with methergoline did not alter the zimelidine-induced attenuation of ethanol intake. Based on these results it is suggested that blockade of 5-hydroxytryptamine uptake produces an attenuation of ethanol intake but not as a result of increased post-synaptic activity.

Reduction of voluntary morphine consumption following treatment with zimelidine

Male Wistar rats were presented with an everyday free choice between water and a morphine-sucrose solution. Following a 5-day baseline period animals were injected with either zimelidine (10 or 20 mg/kg, i.p.), a neuronal serotonin uptake inhibitor, or Ringer's solution (2 ml/kg, i.p.) for 5 consecutive days. Treatment with zimelidine was shown to significantly attenuate morphine drinking suggesting that an increased availability of serotonin may interfere with the positive reinforcing properties of morphine. The results are also discussed in terms of a possible interaction with brain norepinephrine. The possibility that the reinforcing effects of both morphine and ethanol are subserved by common mechanisms is suggested.

Cholera-like diarrhea in Canada. Report of a case associated with enterotoxigenic Escherichia coli and a toxin-producing Aeromonas hydrophila

A 67-year-old Indian patient was admitted with an acute cholera-like illness. Toxigenic Escherichia coli producing both heat-stable and heat-labile enterotoxins grew from cultures of feces. In addition, an Aeromonas hydrophila producing a cytotoxic toxin was also isolated from this patient's feces. The unusual severity of this patient's illness may have resulted from coinfection with these two toxigenic organisms, although any role of the toxin produced by a hydrophila is speculative.