Neoechinulin A as a Promising SARS-CoV-2 Mpro Inhibitor: In Vitro and In Silico Study Showing the Ability of Simulations in Discerning Active from Inactive Enzyme Inhibitors

The COVID-19 pandemic and its continuing emerging variants emphasize the need to discover appropriate treatment, where vaccines alone have failed to show complete protection against the new variants of the virus. Therefore, treatment of the infected cases is critical. This paper discusses the bio-guided isolation of three indole diketopiperazine alkaloids, neoechinulin A (1), echinulin (2), and eurocristatine (3), from the Red Sea-derived Aspergillus fumigatus MR2012. Neoechinulin A (1) exhibited a potent inhibitory effect against SARS-CoV-2 M^pro with IC₅₀ value of 0.47 μM, which is comparable to the reference standard GC376. Despite the structural similarity between the three compounds, only 1 showed a promising effect. The mechanism of inhibition is discussed in light of a series of extensive molecular docking, classical and steered molecular dynamics simulation experiments. This paper sheds light on indole diketopiperazine alkaloids as a potential structural motif against SARS-CoV-2 M^pro. Additionally, it highlights the potential of different molecular docking and molecular dynamics simulation approaches in the discrimination between active and inactive structurally related M^pro inhibitors.     

Pathogenicity of peste des petits ruminants virus isolated from Egyptian goats in Egypt

2 Egyptian goats and Boscat rabbits were experimentally inoculated with peste des petits ruminants (PPR) local Egyptian strain (PPR, Egypt 87). The inoculated animals contracted the disease with minor clinical manifestations, accompanied by rise of neutralizing antibodies to PPR virus. Virus was isolated from ocular and nasal secretions, buffy coat, spleen, and liver. No contact infection was observed between inoculated and healthy goats.     

Sequence and phylogenetic analysis of the non-structural 3A and 3B protein-coding regions of foot-and-mouth disease virus subtype A Iran 05

The A Iran 05 foot-and-mouth disease virus (FMDV) subtype was detected in Iran during 2005 and has proven to be highly virulent. This study was undertaken to focus on molecular and phylogenetic analysis of 3A and 3B coding-regions in the A Iran 05 field isolate. To assess the genetic relatedness of A Iran 05 isolate the nucleotide and predicted amino acid sequences of the 3AB region of type A FMDV isolates were compared with twenty previously described type A FMDV isolates. The phylogenetic tree based on the 672 bp 3AB gene sequences of type A FMDV from thirteen different locations clustered them into five distinct lineages. The A Iran 05 isolate clustered in lineage A along with four type A variants and was closely matched with viruses isolated in Turkey and Pakistan during 2005~2006. The number of protein sequence differences exhibited by each of the isolates revealed that A Iran 05 isolate contains three amino acid substitutions at positions 47 and 119 of 3A and 27 of the 3B coding region. The nucleotide identity between A Iran 05 and the other four isolates of lineage A was estimated to be 98%.     

Potentiality of Soil Mulch and Sorghum Extract to Reduce the Biotic Stress of Weeds with Enhancing Yield and Nutrient Uptake of Maize Crop

Two field trials were conducted in 2018 and 2019 to develop practical and economically efficient weed control programs in corn. The experiment included six treatments (cowpea, rice straw, sorghum extract, hoeing, foramsulfuron herbicide and weedy check). The treatments were arranged in randomized complete block design with four replicates. Findings showed that reduction in total weed number was evident with application of hoeing, cowpea and rice straw in 2018 and 2019 seasons, in addition to foramsulfuron herbicide and sorghum extract in 2019. Cowpea, hoeing, foramsulfuron herbicide and rice straw recorded higher reduction in dry biomass of grassy weeds in both seasons. Reductions in N, P and K uptake by weeds because of rice straw and cowpea treatments were similar to hoeing treatment in both seasons. The increases in ear grain weight and grain yield ha^?1 due to cowpea and hoeing treatments were similar to rice straw one. In 2019 season, cowpea treatment was the superior practice for improving N, P and K uptake of maize, significantly leveling hoeing for K uptake. The values of gross returns and benefit/cost ratio of cowpea and sorghum extract, respectively, were higher than rice straw application. In conclusion, cowpea as a live mulch achieved acceptable weed control in maize by reducing weeds growth and lowering their ability to deplete the soil nutrients. Also, cowpea treatment improves growth and yield of maize with better utilization of nutrients. Thus, cowpea could be exploited as an eco-friendly method of weed management programs in maize cultivation.

     

Effect of indole-acetic acid (IAA) on the development of symptoms caused by <Emphasis Type="Italic">Pythium ultimum</Emphasis> on tomato plants

The effect of indole-acetic acid (IAA) on the development of symptoms caused by Pythium ultimum on tomato plants was investigated using different bioassays. Application of IAA (5 μg ml⁻¹) on tomato seedlings inoculated with P. ultimum did not affect their emergence suggesting that IAA did not affect the severity of Pythium damping-off. However, IAA was shown to influence the development of P. ultimum symptoms on tomato plantlets. Low concentrations of IAA (0–0.1 μg ml⁻¹) within the rhizosphere of plantlets increased the severity of the symptoms caused by P. ultimum, while higher concentrations (10 μg ml⁻¹), applied either by drenching to the growing medium or by spraying on the shoot, reduced the symptoms caused by this pathogen. In addition, the study demonstrated that P. ultimum produces IAA in liquid culture amended with L-tryptophan, tryptamine or tryptophol (200 μg ml⁻¹) and in unamended culture.     

Mass propagation method from the cutting of three dipterocarp species

We developed a vegetative propagation system for mass-producing three dipterocarps species,Shorea selanica Bl.,Shorea leprosula Mig., andShorea platyclados Sloot. This system uses fog evaporative cooling inside a greenhouse to reduce the leaf-to-air vapor pressure deficit (leaf-to-air VPD) inside the propagator, even under high irradiance conditions. This cooling method has no negative influence on medium conditions such as overwetting. A plastic tent propagator combined with this cooling method was used for vegetative propagation experiments. In mass-production experiments, the annual rooting percentages from the cuttings were low in the first 2 years (1997–1998) due to operational problems of the tent propagator (S. selanica, 48–51%;S. leprosula, 56–59%;S. platyclados: 50–63%). A hard cover propagator improved the rooting percentages in the mass-production experiments in 1999 because it made operations easier (S. selanica, 70%;S. leprosula, 77%;S. platyclados, 77%). This system, which uses a combination of fog evaporative cooling and a hard plastic propagator, should be useful for the mass propagation of these dipterocarp planting stocks. This study was carried out under a joint project of the Ministry of Forestry, Indonesia and Komatsu Ltd. The project was supported by Research Association for Reforestation of Tropical Forest (RETROF) organized by Japanese Forestry Agency.     

Effects of methoxyfenozide and pyridalyl on the larval ectoparasitoid Habrobracon hebetor

Habrobracon hebetor Say (Hymenoptera: Braconidae) is an ectoparasitoid that is used for inundative biological control of various lepidopteran insect pests. Lethal and sublethal effects of two biorational insecticides, methoxyfenozide and pyridalyl, were evaluated on H. hebetor under laboratory conditions. The adults were exposed to dry insecticide residues that were applied on glass plates. Bioassays showed that the LC₅₀ values of methoxyfenozide and pyridalyl were 155 and 1,226 μg a.i./ml, respectively. The LT₅₀ values of methoxyfenozide and pyridalyl were 2.1 and 3.3 days, respectively. The effects of methoxyfenozide and pyridalyl on larvae were tested using a dip method with field-recommended concentrations of either insecticide. The emergence rates were reduced by 24.4 and 29.3 % for methoxyfenozide and pyridalyl treatments, respectively. In order to assess the sublethal effects of low-lethal concentrations of methoxyfenozide and pyridalyl, adult wasps were exposed to the LC₃₀ concentration of each insecticide, and demographic parameters of live wasps were recorded. Exposure of adults to low-lethal concentrations (LC₃₀) negatively affected the fecundity, fertility, and sex ratio, and also the intrinsic rate of increase (r _m), finite rate of increase (λ), generation time (T), and doubling time (DT). The longevity and net reproductive rate (R ₀) of H. hebetor were not affected by sublethal exposure to these insecticides. The results showed that despite low acute toxicities of both insecticides on larval and adult stages of H. hebetor, they may negatively affect the population of the parasitoid and interfere in IPM programs.     

Effect of phosphate dissolving bacteria on P-uptake by barley plants grown in a salt affected calcareous soil

In a pot experiment the effect of inoculation of a salt affected calcareous soil with phosphate dissolving bacteria (PDB) on dehydrogenase activity and P-uptake by barley plants was investigated. Four levels of artificial salinity were used, i. e., 0.2, 0.4, 0.8 and 1.2 % total soluble salts. Inoculation increased PDB in all treatments, but it did not affect the microbial activity in the soil as represented by dehydrogenase activity. The higher the salt level the lower the counts of PDB and dehydrogenase activity in the soil. A positive significant difference was recorded in P-uptake as a result of inoculation and a negative one as a result of increasing salinity.     

Induction of a malathion-resistant strain in the common predacious mite Amblyseius cydnodactylon (Acari: Phytoseiidae)

This study demonstrates a laboratory induction of a malathion - resistant strain in Amblyseius cydnodactylon Shehata & Zaher and effect of selection on reproduction. Initially 500 sensitive females obtained from a laboratory mass culture were exposed to malathion at LC70. Subsequent selections were conducted every two generations at progressive LC70 values and number of eggs/female/day was recorded at each selection. Experiments were carried out under laboratory conditions of 24-28°C and 70-80 % R. H. The LC70 in the parent generation was 5.19 ppm and increased to 20 ppm in F4 selection generation. The dosage mortality relationships continued to increase up to a maximum of 282.3 ppm in F16. The rate of developing resistance increased from 1.75 folds in F2 to 1.97 folds in F4 and gradually reached a maximum of 54.39 folds in F16. There was an obvious decrease in reproduction corresponded to increasing resistance. For example, the number of eggs/female/day in F 16 was 8 eggs, contrasting 3 eggs in the parent generation.     

Bioactive Compounds from the Red Sea Marine Sponge Hyrtios Species

In continuation of our search for drug leads from Red Sea sponges we have investigated the ethyl acetate fraction of the organic extract of the Red Sea sponge Hyrtios species. Bioassay-directed fractionation of the active fraction resulted into the identification of three new alkaloids, hyrtioerectines D–F (1–3). Hyrtioerectines D–F belong to the rare marine alkaloids in which the indole and β-carboline fragments of the molecule are linked through C-3/C-3 of both moieties. The structures of the isolated compounds were established based on different spectroscopic data including UV, IR, 1D and 2D NMR (COSY, HSQC, and HMBC) and high-resolution mass spectral studies. The antimicrobial activity against several pathogens and the free radical scavenging activity of the compounds using DPPH reagent were evaluated. In addition, the growth inhibitory activity of the compounds against three cancer cell lines was also evaluated. Hyrtioerectines D–F (1–3) displayed variable antimicrobial, free radical scavenging and cancer growth inhibition activities. Generally, compounds 1 and 3 were more active than compound 2.