Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 μM and 66 μM. In addition, eight compounds inhibited PLpro with IC50 ranging from 1.7 μM to 46 μM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.

Enzyme Linked Immunosorbent Assay (ELISA)

Enzyme immunoassay (EIA) and enzyme-linked immunosorbent assay (ELISA) are both widely used as diagnostic tools in medicine and as quality control measures in many industries. ELISA has been the system of choice when testing soluble antigens and antibodies. EIA / ELISA uses the basic immunological concept of antigen binding to specific antibodies, which allows the detection of small amounts of antigens such as proteins, peptides, hormones or antibodies in fluid samples. In all protocols, solid-phase reagents are incubated with secondary or tertiary reactants covalently coupled with the enzyme. The unbound conjugate is washed and a chromogenic or fluorogenic substrate is added.

Spatial patterns of ectoenzymatic kinetics in relation to biogeochemical properties in the Mediterranean Sea and the concentration of the fluorogenic substrate used

Ectoenzymatic activity, prokaryotic heterotrophic abundances and production were determined in the Mediterranean Sea. Sampling was carried out in the sub-surface, the deep chlorophyll maximum layer (DCM), the core of the Levantine intermediate waters and in the deeper part of the mesopelagic layers. Michaelis–Menten kinetics were assessed using a large range of concentrations of fluorogenic substrates (0.025 to 50 µM). As a consequence, Km (Michaelis–Menten half-saturation constant) and Vm (maximum hydrolysis velocity) parameters were determined for both low- and high-affinity enzymes for alkaline phosphatase, aminopeptidase (LAP) and β-glucosidase (βGLU). Based on the constant derived from the high-LAP-affinity enzyme (0.025–1 µM substrate concentration range), in situ hydrolysis of N proteins contributed 48 % ± 30 % to the heterotrophic bacterial nitrogen demand within the epipelagic layers and 180 % ± 154 % in the Levantine intermediate waters and the upper part of the mesopelagic layers. The LAP hydrolysis rate was higher than bacterial N demand only within the deeper layer and only when considering the high-affinity enzyme. Based on a 10 % bacterial growth efficiency, the cumulative hydrolysis rates of C proteins and C polysaccharides contributed on average 2.5 % ± 1.3 % to the heterotrophic bacterial carbon demand in the epipelagic layers sampled (sub-surface and DCM). This study clearly reveals potential biases in current and past interpretations of the kinetic parameters for the three enzymes tested based on the fluorogenic-substrate concentration used. In particular, the LAP / βGLU enzymatic ratios and some of the depth-related trends differed between the use of high and low concentrations of fluorogenic substrates.

An Engineered Reporter Phage for the Fluorometric Detection of Escherichia coli in Ground Beef

Despite enhanced sanitation implementations, foodborne bacterial pathogens still remain a major threat to public health and generate high costs for the food industry. Reporter bacteriophage (phage) systems have been regarded as a powerful technology for diagnostic assays for their extraordinary specificity to target cells and cost-effectiveness. Our study introduced an enzyme-based fluorescent assay for detecting the presence of E. coli using the T7 phage engineered with the lacZ operon which encodes beta-galactosidase (β-gal). Both endogenous and overexpressed β-gal expression was monitored using a fluorescent-based method with 4-methylumbelliferyl β-d-galactopyranoside (MUG) as the substrate. The infection of E. coli with engineered phages resulted in a detection limit of 10 CFU/mL in ground beef juice after 7 h of incubation. In this study, we demonstrated that the overexpression of β-gal coupled with a fluorogenic substrate can provide a straightforward and sensitive approach to detect the potential biological contamination in food samples. The results also suggested that this system can be applied to detect E. coli strains isolated from environmental samples, indicating a broader range of bacterial detection.

A New Fluorogenic Substrate for Granzyme B Based on Fluorescence Resonance Energy Transfer

The synthesis and characterization of a new fluorogenic substrate for granzyme B (GzmB) is reported. The substrate design was based on the fluorescence resonance energy transfer (FRET) principle using 5-(2′-aminoethyl)aminonaphthalene sulfonic acid (Edans) and 4-[[4′-(N,N-dimethylamino)phenyl]diazenyl]benzoic acid (Dabcyl) as a donor–acceptor pair, linked to a specific sequence for GzmB (AAD), with an additional amino acid as the anchoring point (K). The tetrapeptide was synthesized by microwave-assisted solid-phase peptide synthesis (MW-SPPS) and coupled to Dabcyl and Edans at its N- and C-termini, respectively. The obtained probe was purified by semi-preparative HPLC and characterized by NMR, UV/Vis absorption and fluorescence spectroscopy and mass spectrometry.

Gaucher disease neonatal screening experience with using artificial fluorogenic substrate

Важность неонатального скрининга болезни Гоше во многом обусловлена созданием эффективной патогенетически обоснованной терапии. Постановка диагноза строится на обнаружении снижения активности фермента бета-глюкоцереброзидазы в лейкоцитах периферической крови. Newborn screening of Gaucher diseases is important because of the development of treatment options that improve clinical outcome. The diagnosis of Gaucher disease relies on demonstration of deficient glucocerebrosidase enzyme activity in peripheral blood leukocytes.

A Novel Highly Sensitive Method for Measuring Inflammatory Neural-Derived APC Activity in Glial Cell Lines, Mouse Brain and Human CSF

Background: Neural inflammation is linked to coagulation. Low levels of thrombin have a neuroprotective effect, mediated by activated protein C (APC). We describe a sensitive novel method for the measurement of APC activity at the low concentrations found in neural tissue. Methods: APC activity was measured using a fluorogenic substrate, Pyr-Pro-Arg-AMC, cleaved preferentially by APC. Selectivity was assessed using specific inhibitors and activators. APC levels were measured in human plasma, in glia cell lines, in mice brain slices following mild traumatic brain injury (mTBI) and systemic lipopolysaccharide (LPS) injection, and in cerebrospinal fluid (CSF) taken from viral meningoencephalitis patients and controls. Results: Selectivity required apixaban and alpha-naphthylsulphonylglycyl-4-amidinophenylalanine piperidine (NAPAP). APC levels were easily measurable in plasma and were significantly increased by Protac and CaCl2. APC activity was significantly higher in the microglial compared to astrocytic cell line and specifically lowered by LPS. Brain APC levels were higher in posterior regions and increased by mTBI and LPS. Highly elevated APC activity was measured in viral meningoencephalitis patients CSF. Conclusions: This method is selective and sensitive for the measurement of APC activity that significantly changes during inflammation in cell lines, animal models and human CSF.