Identification of Four New Chemical Series of Small Drug-Like Natural Products as Potential Neuropilin-1 Inhibitors by Structure-Based Virtual Screening: Pharmacophore-Based Molecular Docking and Dynamics Simulation.

Neuropilin-1 (NRP-1), a surface transmembrane glycoprotein, is one of the most important co-receptors of VEGF-A165 (vascular endothelial growth factor) responsible for pathological angiogenesis. In general, NRP-1 overexpression in cancer correlates with poor prognosis and more tumor aggressiveness. NRP-1 role in cancer has been mainly explained by mediating VEGF-A165-induced effects on tumor angiogenesis. NRP-1 was recently identified as a co-receptor and an independent gateway for SARS-CoV-2 through binding subunit S2 of Spike protein in the same way as VEGF-A165. Thus, NRP-1 is of particular value as a target for cancer therapy and other angiogenesis-dependent diseases as well as for SARS-CoV-2 antiviral intervention. Herein, The Super Natural II, the largest available database of natural products (∼0.33 M), pre-filtered with drug-likeness criteria (absorption, distribution, metabolism and excretion/toxicity), was screened against NRP-1. NRP-1/VEGF-A165 interaction is one of protein-protein interfaces (PPIs) known to be challenging when approached in-silico. Thus, a PPI-suited multi-step virtual screening protocol, incorporating a derived pharmacophore with molecular docking and followed by MD (molecular dynamics) simulation, was designed. Two stages of pharmacophorically constrained molecular docking (standard and extra precisions), a mixed Torsional/Low-mode conformational search and MM-GBSA ΔG binding affinities calculation, resulted in the selection of 100 hits. These 100 hits were subjected to 20 ns MD simulation, that was extended to 100 ns for top hits (20) and followed by post-dynamics analysis (atomic ligand-protein contacts, RMSD, RMSF, MM-GBSA ΔG, Rg, SASA and H-bonds). Post-MD analysis showed that 19 small drug-like nonpeptide natural molecules, grouped in four chemical scaffolds (purine, thiazole, tetrahydropyrimidine and dihydroxyphenyl), well verified the derived pharmacophore and formed stable and compact complexes with NRP-1. The discovered molecules are promising and can serve as a base for further development of new NRP-1 inhibitors.

Improving zinc phytoremediation characteristics in Salix pedicellata with a new acclimation approach.

Some species of Salix sp. (willows) are a potential phytoremediator that can accumulate substantial contents of mineral elements and, therefore, to detoxify soils contaminated with pollutants and heavy metals such as the zinc (Zn). However, high concentrations of Zn inhibit plant growth and reduce biomass production in plants. In an attempt to overcome this inconvenience and to enhance plant tolerance to Zn toxicity, we tested a new tolerance induction approach by acclimation in two clones of Salix pedicellata, named SPK-12 and SP-K20. The approach comprises two successive phases. The first is a "tolerance induction phase" consisting of gradual exposure of plants to low concentrations of Zn sulfate (ZnSO4) at regular intervals until reaching DI100 (ZnSO4 inhibitory concentration). And, the second is a "tolerance maintenance phase" to uphold the acquired tolerance to Zn toxicity. The SP-K20 clone was acclimated to DI100 threshold over 33 days without noticeable symptoms of chlorosis or growth inhibition. Compared to controls, the SP-K20 clone was able to accumulate high concentrations of Zn, suggesting that phytoremediation abilities of S. pedicellata have been improved throughout the applied approach. Acclimated Salix plants might thus improve metal phytoextraction in heavily polluted soils without biomass growth inhibition.

Tropane alkaloids GC/MS analysis and low dose elicitors' effects on hyoscyamine biosynthetic pathway in hairy roots of Algerian Datura species.

Plant secondary metabolites play a major role in plant adaptation to stress. Species belonging to Solanaceae family and Datura genus produce tropane alkaloids: D. stramonium, D. tatula and D. innoxia. These species are cultivated for their hyoscyamine (HS) content, whence the interest of this study to induce transformed roots of these species with strain A4 of Agrobacterium rhizogenes. Hairy roots (HRs) of Datura were established at high frequency by infecting vitroplants. All HRs (343 independent lines) were next employed to study the production of HS and growth. A screening of HRs alkaloid content by GC/MS is performed; it reveals, for the first time, the production of 13 alkaloids by the selected root lines. The selection of high productive line offers an interesting option to enhance the productivity. As HS is the dominant compound, the lines of Datura species were selected for their characteristics for biomass and HS production. The elicitors salicylic acid (SA) and acetyl salicylic acid (ASA) were also used to increase HS production. The results showed that the optimal concentration of the two elicitors (AS and ASA) was 0.1 mM. The highest HS content (17.94 ± 0.14 mg g-1 D.W.) obtained in HRs of D. tatula treated with 0.1 mM of acetyl salicylic acid.

The Desirability Optimization Methodology; a Tool to Predict Two Antagonist Responses in Biotechnological Systems: Case of Biomass Growth and Hyoscyamine Content in Elicited Datura starmonium Hairy Roots.

BACKGROUND: The use of the desirability function approach combined with the response surface methodology (RSM), also called Desirability Optimization Methodology (DOM), has been successfully applied to solve medical, chemical, and technological questions. It is particularly efficient for the determination of the optimal conditions in natural or industrial processes involving different factors leading to the antagonist responses. OBJECTIVES: Surprisingly, DOM has never been applied to the research programs devoted to the study of plant responses to the complex environmental changes, and thus to biotechnological questions. MATERIALS AND METHODS: In this article, DOM is used to study the response of Datura stramonium hairy roots (HRs), obtained by genetic transformation with Agrobacterium rhizogenes A4 strain, subjected to the jasmonate treatments. RESULTS: Antagonist effects on the growth and tropane alkaloid biosynthesis are confirmed. With a limited number of experimental conditions, it is shown that 0.06 mM jasmonic acid (JA) applied for 24 h leads to an optimal compromise. Hyoscyamine levels increase by up to 290% after 24 h and this treatment does not significantly inhibit biomass growth. CONCLUSIONS: It is thus demonstrated that the use of DOM can efficiently - with a minimized number of replicates - leads to the optimization of the biotechnological processes.

Genetic variation and structure of maize populations from Saoura and Gourara oasis in Algerian Sahara.

BACKGROUND: The ability of maize populations/landraces to tolerate drastically extreme environments over the past four centuries in Algeria leads to characterize these genetic resources for germplasm management as well as the identification of the best landraces useful for genetic improvement. Thus, the aim of the present work was a fingerprinting of an Algerian maize collection (47 landraces) from Saharan oasis by using 24 agro-morphological traits and18 Simple Sequence Repeats to evaluate genetic diversity and population structure. RESULTS: Phenotypic traits showed large significant variation in which earliness, plant size, ear and kernel features and crop yield appeared the most discriminant traits among landraces by using principal component analysis (PCA). One hundred ninety-seven different alleles were detected with a high mean number of allele per locus (10.9). The selected SSR were highly informative with PIC values > 0.65 as well as an overall genetic diversity (0.47) highlighting a broad genetic variability in the analyzed landraces. Genetic structure analysis revealed a high genetic differentiation among the 47 maize landraces with an overall Fst value (0.33). Cluster analysis for morphological traits as well as for SSR markers grouped the 47 Algerian populations regardless their geographic origin. CONCLUSIONS: Maize from Algerian desert harbors a wide genetic diversity offering a source of novel/unique alleles useful for maize breeding programs to face the ongoing and future major challenge, the climate changes.

Desiccation-Enhanced Maturation and Germination of Date Palm Somatic Embryos Derived from Cell Suspension Culture.

In vitro plant regeneration via somatic embryogenesis is a powerful tool for rapid, large-scale production of healthy true-to-type plants. This approach is suitable to preserve existing natural genetic variability and propagation of variability generated from genetic improvement programs, including crossing, somaclonal variation, mutagenesis, and somatic hybridization. This chapter outlines a simplified protocol for date palm regeneration via somatic embryogenesis induced in cell suspension cultures. In this protocol, culture medium composition is manipulated, including plant growth regulators and solid (addition of agar) and liquid media to achieve reduction of production cycle of somatic embryogenesis, which increases the multiplication rate of embryogenic callus and improves the quantity and quality of somatic embryos.

Microcalli Induction in Protoplasts Isolated from Embryogenic Callus of Date Palm.

Date palm (Phoenix dactylifera L.) production is severely hampered due to several pests and diseases. Biotechnological tools such as protoplast fusion appear as an alternative to ensure rapid genetic improvement and multiplication of this species. However, establishment of an effective system of plant regeneration from protoplasts culture is a prerequisite for date palm somatic hybridization. In this chapter, we describe an effective protocol to induce microcalli in protoplasts isolated from nodular callus of important Algerian date palm cultivars. In this protocol, the main factors influencing the isolation (i.e., enzymatic solution, mannitol concentration, duration, and mode of maceration) of protoplasts from the calli of Algerian date palm cultivars were optimized. Purified protoplasts were cultured on a semisolid medium supplemented with a hormonal balance of auxin and cytokinin to obtain microcalli formation.

Screening and kinetic studies of catharanthine and ajmalicine accumulation and their correlation with growth biomass in Catharanthus roseus hairy roots.

Context Catharanthus roseus (L.) G. Don (Apocynaceae) is still one of the most important sources of terpene indole alkaloids including anticancer and hypertensive drugs as vincristine and vinblastine. These final compounds have complex pathway and many enzymes are involved in their biosynthesis. Indeed, ajmalicine and catharanthine are important precursors their increase can lead to enhance levels of molecules of interest. Objective This study aims at selecting the highest yield of hairy root line(s) and at identifying best times for further treatments. We study kinetics growth and alkaloids (ajmalicine and catharanthine) accumulation of three selected hairy root lines during the culture cycle in order to determine the relationship between biomass production and alkaloids accumulation. Materials and methods Comparative analysis has been carried out on three selected lines of Catharanthus roseus hairy roots (LP10, LP21 and L54) for their kinetics of growth and the accumulation of ajamalicine and catharanthine, throughout a 35-day culture cycle. The methanolic extract for each line in different times during culture cycle is analyzed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Results Maximum accumulation of the alkaloids is recorded for LP10 line in which the peak of ajmalicine and catharanthine accumulation reached to 3.8 and 4.3 mg/g dry weight (DW), respectively. This increase coincides with an exponential growth phase. Discussion and conclusion Our results suggest that the evolution of accumulation of ajmalicine and catharanthine are positively correlated with the development of the biomass growth. Significantly, for LP10 line the most promising line to continue optimizing the production of TIAs. Additionally, the end of exponential phase remains the best period for elicitor stimuli.

A Pseudomonas strain isolated from date-palm rhizospheres improves root growth and promotes root formation in maize exposed to salt and aluminum stress.

The aim of this study was to evaluate the effectiveness of Pseudomonas fluorescens 002 (P.f.002.), isolated from the rhizosphere of date palms from the Ghardaia region in the Algerian Sahara, to promote root growth of two varieties of maize under conditions of salt and aluminum stress. Primary roots of 5-day-old seedlings were inoculated with P.f.002., and seedlings were then grown under both control and stressed conditions. Primary, lateral, and seminal root lengths and numbers, as well as root dry mass, were evaluated. P.f.002 increased all parameters measured under both salt and aluminum stress. Hence, the use of P.f.002 may represent an important biotechnological approach to decrease the impact of salinity and acidity in crops.

A simplified Protocol to Induce Callogenesis in Protoplasts of Date Palm (Phoenix dactylifera L.) Cultivars.

BACKGROUND: In Algeria, date palm is currently confronted to the Bayoud disease. Biotechnological tools such as protoplastsfusion can appear as an alternative to ensure rapid multiplication and improvement of this species. OBJECTIVES: Callogenesis induction in protoplasts isolated from embryogenic callus of three date palm cultivars. MATERIALS AND METHODS: Some factors influencing the isolation and culture of protoplasts segregated from the calli of three date palm (Phoenix dactylifera L.) cultivars (Deglet Nour, Akerbouch and Degla Beida) were studied. Protoplasts of each cultivar were cultured on a semi-solid medium supplemented with various hormonal balances. RESULTS: Maceration with an enzymatic solution containing 1.5% cellulase and 1% macerozyme R10 in the presence of 0.5 M mannitol for more than 16 h with gentle agitation allows isolation of a great number of viable protoplasts. In addition, purification of protoplasts on a cushion of 21 or 25% sucrose was effective in cell debris removal and maximum recovery. The culture of isolated protoplasts on a semi-solidified Murashige and Skoog medium, with 0.3% agarose, 2 mg. L-1 2,4-D and 0.5 mg.L-1 BAP allowed good viable protoplast maintenance as well as cell wall regeneration. After more than two months of culture, cell divisions were still occurring and microcalli became visible to the naked eye, containing a large number of cells. CONCLUSIONS: The developed protocol can be useful for application of somatic hybridization to improve date palm cultivars.