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.     

Control of adventitious root formation: insights into synergistic and antagonistic hormonal interactions

Plants have evolved sophisticated root systems that help them to cope with harsh environmental conditions. They are typically composed of a primary root and lateral roots (LRs), but may also include adventitious roots (ARs). Unlike LRs, ARs may be initiated not only from pericycle cells, but from various cell types and tissues depending on the species. Phytohormones, together with many other internal and external stimuli, coordinate and guide every step of AR formation from the first event of cell reprogramming until emergence and outgrowth. In this review, we summarize recent advances in the molecular mechanisms controlling AR formation and highlight the main hormonal cross talk involved in its regulation under different conditions and in different model systems.     

Multi-layer MoS2-Based Plasmonic Gold Nanowires at Near-Perfect Absorption for Energy Harvesting

One of the biggest challenges in relation to the modernistic vision of smart city technology is to provide confident autonomous energy, notably in terms of power storage. If you want to change an existing lifestyle, you cannot ignore the basic concepts collected from basic physics. The subject of Metamaterials stands for an important research area that can be explored and used to come up with unparalleled ideas about the properties and functions that are completely absent from natural materials. In contrast to other bold technologies, combining a simple layered surface with appropriate material selection makes it possible to pattern and manufacture new types of solar cells that work in a wide frequency range. In this article, we propose a simple method to boost the coupling interaction between metallic gold nanowires with multiple MoS₂ layers. The innovation of this work is that the thickness layer changes have great stability in the influence of the absorption performance and electric field distribution in the visible light and near-infrared spectra. Therefore, this new design can be seen as very important in many fields from sensing to solar cell applications.

     

Genome editing of potato using CRISPR technologies: current development and future prospective

Potato (Solanum tuberosum L.) has tremendous significance due to its nutritional quality. The mounting pressure of increasing population further reinforces its importance as potato is believed to be a vital crop to meet food needs for population growth. Although conventional approaches of breeding, irradiation/mutagens and introgression of quality and yield related traits have improved potato yield, biotic and abiotic stresses continue to impose crop damages. Modern tools such as CRISPR/Cas have assisted plant scientists in accelerating breeding processes by providing new, simple, versatile and robust technologies. These tools make it possible to eliminate traits that are involved in negative regulation of quality and yield parameters. Besides that, genes of interest can also be introduced in close proximity to specific loci that may remain linked throughout the generations. This review focuses on the endeavors, applications and prospects of CRISPR/Cas-based approaches in potato with the potential to increase sustainable crop productivity.

     

Starvation-Induced Multiresistance in Enterococcus faecalis JH2-2

Compared with growing bacteria, carbohydrate-starved cells of Enterococcus faecalis show development of a multiresistance state against heat, H₂O₂, acid, and ethanol, but not against UV irradiation. The kinetics of acquisition of resistance is different according to the stress. Three hours of starvation provide maximal resistance against ethanol, while the tolerance to heat, H₂O₂, and acid increases progressively with the duration of starvation. Chloramphenicol treatment does not abolish the ethanol tolerance. Protein synthesis inhibition during the transitional growth phase and the first hours of starvation partially inhibit the acquisition of heat and oxidative resistances. Antibiotic treatment after 3 h of starvation does not affect the increase of these resistances. We suggest that synthesis of specific proteins revealed by 2-D gel analysis in the first 3 h of starvation, followed by a second mechanism related to protein degradation or alteration, is necessary for acquisition of maximal resistance towards heat and oxidative stresses.     

Plasmid Transfer by Electroporation and Conjugation in Tetragenococcus and Pediococcus Genera and Evidence of Plasmid-Linked Metabolic Traits

Various strains of Pediococcus genus were successfully transformed by electroporation using the broad host-range plasmid pSA3 and the lactococcal Rep22 based-replicon pUCB304. Failure to transform Tetragenococcus strains by electroporation have led to use conjugation as an alternative plasmid DNA transfer mechanism. Intergeneric matings conducted with the broad host-range conjugative plasmid pVA797 from Lactococcus lactis subsp. lactis SL2/797A to Tetragenococcus halophilus and Pediococcus pentosaceus strains have shown that Tetragenococcus strains are not impervious to plasmid DNA transfer. Plasmid and metabolic profiles of wild and mutant strains of Pediococcus pentosaceus NCDO990 have shown that many metabolic traits including lactose utilization are plasmid linked.     

The Lactic Acid Stress Response of Lactococcus lactis subsp. lactis

The lactic acid tolerance response (LATR) of the lactic acid bacterium Lactococcus lactis subsp. lactis has been studied. A dramatic increase in survival to a severe acid stress (pH 3.9) was obtained by preexposing the cells for 30 min to a mildly acid shock at pH 5.5. Whole-cell protein extract analysis revealed that during the acid tolerance response 33 polypeptides are induced over the level of naive cells. Among these are the major heat shock proteins DnaK and GroEL. In conjunction with a previous report (Hartke et al. 1994), the results establish that L. lactis can adapt to lactic acid exposure in two different ways: a logarithmic phase LATR, which may be activated by protons, and a stationary-phase LATR, which needs no activation by protons. Both systems are independent of de novo protein synthesis. Received: 8 February 1996 / Accepted: 11 March 1996