Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein,Mpro and PLpro of SARS-CoV-2: Protein–Protein Interactions,Dynamics Simulations and Free Energy Calculations

The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (−16.8 ± 0.02 kcal/mol, −12.3 ± 0.03 kcal/mol and −13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (M^pro) and the papainlike protease (PL^pro) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson–Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.     

Direct CO2 capture and conversion to fuels on magnesium nanoparticles under ambient conditions simply using water

Converting CO₂ directly from the air to fuel under ambient conditions is a huge challenge. Thus, there is an urgent need for CO₂ conversion protocols working at room temperature and atmospheric pressure, preferentially without any external energy input. Herein, we employ magnesium (nanoparticles and bulk), an inexpensive and the eighth-most abundant element, to convert CO₂ to methane, methanol and formic acid, using water as the sole hydrogen source. The conversion of CO₂ (pure, as well as directly from the air) took place within a few minutes at 300 K and 1 bar, and no external (thermal, photo, or electric) energy was required. Hydrogen was, however, the predominant product as the reaction of water with magnesium was favored over the reaction of CO₂ and water with magnesium. A unique cooperative action of Mg, basic magnesium carbonate, CO₂, and water enabled this CO₂ transformation. If any of the four components was missing, no CO₂ conversion took place. The reaction intermediates and the reaction pathway were identified by ¹³CO₂ isotopic labeling, powder X-ray diffraction (PXRD), nuclear magnetic resonance (NMR) and in situ attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and rationalized by density-functional theory (DFT) calculations. During CO₂ conversion, Mg was converted to magnesium hydroxide and carbonate, which may be regenerated. Our low-temperature experiments also indicate the future prospect of using this CO₂-to-fuel conversion process on the surface of Mars, where CO₂, water (ice), and magnesium are abundant. Thus, even though the overall process is non-catalytic, it could serve as a step towards a sustainable CO₂ utilization strategy as well as potentially being a first step towards a magnesium-driven civilization on Mars.

We demonstrated the use of magnesium nanoparticles (and bulk) to convert CO₂ (pure & also from the air) to methane, methanol, formic acid and green cement without external energy within a few minutes, using only water as the sole hydrogen source.     

ABCAttack: A Gradient-Free Optimization Black-Box Attack for Fooling Deep Image Classifiers

The vulnerability of deep neural network (DNN)-based systems makes them susceptible to adversarial perturbation and may cause classification task failure. In this work, we propose an adversarial attack model using the Artificial Bee Colony (ABC) algorithm to generate adversarial samples without the need for a further gradient evaluation and training of the substitute model, which can further improve the chance of task failure caused by adversarial perturbation. In untargeted attacks, the proposed method obtained 100%, 98.6%, and 90.00% success rates on the MNIST, CIFAR-10 and ImageNet datasets, respectively. The experimental results show that the proposed ABCAttack can not only obtain a high attack success rate with fewer queries in the black-box setting, but also break some existing defenses to a large extent, and is not limited by model structure or size, which provides further research directions for deep learning evasion attacks and defenses.     

Synthesis of Carvacrol Derivatives as Potential New Anticancer Agent against Lung Cancer

Lung cancer remains a major public health concern among all cancer diseases due to the toxicity and side-effects of the available commercially synthesized drugs. Natural product-derived synthesized anticancer drugs are now of promising interest to fight against cancer death. Carvacrol is a major component of most essential oil-bearing plants with potential pharmacological activity, especially against various cancer cell lines. Among the other organometallic compounds, copper complexes have been reported to be effective anticancer agents against various cancer cell lines, especially lung and leukemia cancers, due to the nontoxic nature of copper in normal cells since it is an endogenic metal. In this study, we synthesized three carvacrol derivatives, i.e., carvacrol aldehyde, Schiff base, and copper–Schiff base complex, through an established synthesis protocol and characterized the synthesized product using various spectroscopic techniques. The synthesized derivatives were evaluated for in vitro cytotoxic activity against different cancer cell lines, including human lung cancer (A549) and human fibroblast (BALB-3T3). Our findings showed that the copper–Schiff base complex derived from carvacrol inhibited the proliferation and migration of the A549 cell lines in a dose-dependent manner. This activity might be due to the inhibition of cell proliferation and migration at the G₂/M cell-cycle phase, as well as apoptosis, possibly through the activation of the mitochondrial apoptotic pathway. To our knowledge, this is the first report on the activity of the copper–Schiff base complex of carvacrol against A549 cell lines. Our result highlights that a new synthesized copper complex from carvacrol could be a novel potential drug in the treatment of lung cancer.     

Delicate Balance of Non-Covalent Forces Govern the Biocompatibility of Graphitic Carbon Nitride towards Genetic Materials

Despite a plethora of suggested technological and biomedical applications, the nanotoxicity of two-dimensional (2D) graphitic carbon nitride (g-C₃N₄) towards biomolecules remains elusive. To address this issue, we employ all-atom classical molecular dynamics simulations and investigate the interactions between nucleic acids and g-C₃N₄. It is revealed that, toxicity is modulated through a subtle balance between electrostatic and van der Waals interactions. When the exposed nucleobases interact through predominantly short-ranged van der Waals and π–π stacking interactions, they get deviated from their native disposition and adsorb on the surface, leading to loss of self-stacking and intra-quartet H-bonding along with partial disruption of the native structure. In contrast, for the interaction with double-stranded structures of both DNA and RNA, long-range electrostatics govern the adsorption phenomena since the constituent nucleobases are relatively concealed and wrapped, thereby resulting in almost complete preservation of the nucleic acid structures. Construction of free energy landscapes for lateral translation of adsorbed nucleic acids suggests decent targeting specificity owing to their restricted movement on g-C₃N₄. The release times of nucleic acids adsorbed through predominant electrostatics are significantly less than those adsorbed through stacking with the surface. It is therefore proposed that g-C₃N₄ would induce toxicity towards any biomolecule having bare residues available for strong van der Waals and π–π stacking interactions relative to those predominantly interacting through electrostatics.     

An NHC-Stabilised Phosphinidene for Catalytic Formylation: A DFT-Guided Approach

In recent years, the applications of low-valent main group compounds have gained momentum in the field of catalysis. Owing to the accessibility of two lone pairs of electrons, NHC-stabilised phosphinidenes have been found to be excellent Lewis bases; however, they cannot yet be used as catalysts. Herein, an NHC-stabilised phosphinidene, 1,3-dimethyl-2-(phenylphosphanylidene)-2,3-dihydro-1H imidazole (1), for the activation of CO₂ is reported.A closer inspection of the CO₂ activation process by DFT calculations along with intrinsic bond orbital analysis shows that phosphinidene is associated with phenylsilane through a noncovalent π-π interaction between two phenyl rings which activates the Si−H bond facilitating hydride transfer to the CO₂ molecule. Detailed DFT studies along with spectroscopic experiments were combined to understand the mechanism of CO₂ activation and its catalytic reductive functionalisation leading to the formylation of a range of chemically inert primary amides under mild reaction conditions.     

Minimally deformed charged stellar model by gravitational decoupling in 5D Einstein–Gauss–Bonnet gravity

The European Physical Journal C - EOS is an open-source software for a variety of computational tasks in flavor physics. Its use cases include theory predictions within and beyond the Standard...     

Charged thin-shell gravastars in noncommutative geometry

In this paper we construct a charged thin-shell gravastar model within the context of noncommutative geometry. To do so, we choose the interior of the nonsingular de Sitter spacetime with an exterior charged noncommutative solution by cut-and-paste technique and apply the generalized junction conditions. We then investigate the stability of a charged thin-shell gravastar under linear perturbations around the static equilibrium solutions as well as the thermodynamical stability of the charged gravastar. We find the stability regions, by choosing appropriate parameter values, located sufficiently close to the event horizon.