Bisindolylmaleimide IX: a Novel Anti-SARS-CoV2 Agent Targeting Viral Main Protease 3CLpro Demonstrated by Virtual Screening Pipeline and In-Vitro Validation Assays

SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2′-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = 5903). The screening was performed against viral targets using three sequential docking modes (i.e., HTVS, SP, and XP). Virtual screening identified ∼290 potential inhibitors based on the criteria of energy, docking parameters, ligand, and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. The top lead from each target pool was further subjected to molecular dynamics simulation using the Desmond module. The resulting top eight hits were tested for their SARS-CoV-2 anti-viral activity in-vitro. Among these, a known inhibitor of protein kinase C isoforms, Bisindolylmaleimide IX (BIM IX), was found to be a potent inhibitor of SARS-CoV-2. Further, target validation through enzymatic assays confirmed 3CLpro to be the target. This is the first study that has showcased BIM IX as a COVID-19 inhibitor thereby validating our pipeline

Defects, Dopants and Lithium Mobility in Li ₉ v ₃ (P ₂ O ₇ ) ₃ (PO ₄ ) ₂

Layered Li9V3(P2O7)3(PO4)2 has attracted considerable interest as a novel cathode material for potential use in rechargeable lithium batteries. The defect chemistry, doping behavior and lithium diffusion paths in Li9V3(P2O7)3(PO4)2 are investigated using atomistic scale simulations. Here we show that the activation energy for Li migration via the vacancy mechanism is 0.72 eV along the c-axis. Additionally, the most favourable intrinsic defect type is Li Frenkel (0.44 eV/defect) ensuring the formation of Li vacancies that are required for Li diffusion via the vacancy mechanism. The only other intrinsic defect mechanism that is close in energy is the formation of anti-site defect, in which Li and V ions exchange their positions (1.02 eV/defect) and this can play a role at higher temperatures. Considering the solution of tetravalent dopants it is calculated that they require considerable solution energies, however, the solution of GeO2 will reduce the activation energy of migration to 0.66 eV

Defects, Dopants and Sodium Mobility in Na₂MnSiO₄

Sodium manganese orthosilicate, Na2MnSiO4, is a promising positive electrode material in rechargeable sodium ion batteries. Atomistic scale simulations are used to study the defects, doping behaviour and sodium migration paths in Na2MnSiO4. The most favourable intrinsic defect type is the cation anti-site (0.44 eV/defect), in which, Na and Mn exchange their positions. The second most favourable defect energy process is found to be the Na Frenkel (1.60 eV/defect) indicating that Na diffusion is assisted by the formation of Na vacancies via the vacancy mechanism. Long range sodium paths via vacancy mechanism were constructed and it is confirmed that the lowest activation energy (0.81 eV) migration path is three dimensional with zig-zag pattern. Subvalent doping by Al on the Si site is energetically favourable suggesting that this defect engineering stratergy to increase the Na content in Na2MnSiO4 warrants experimental verification

Li2SnO3 as a Cathode Material for Lithium-ion Batteries:Defects, Lithium Ion Diffusion and Dopants

Tin-based oxide Li2SnO3 has attracted considerable interest as a promising cathode material for potential use in rechargeable lithium batteries due to its high- capacity. Static atomistic scale simulations are employed to provide insights into the defect chemistry, doping behaviour and lithium diffusion paths in Li2SnO3. The most favourable intrinsic defect type is Li Frenkel (0.75 eV/defect). The formation of anti-site defect, in which Li and Sn ions exchange their positions is 0.78 eV/defect, very close to the Li Frenkel. The present calculations confirm the cation intermixing found experimentally in Li2SnO3. Long range lithium diffusion paths via vacancy mechanisms were examined and it is confirmed that the lowest activation energy migration path is along the c-axis plane with the overall activation energy of 0.61 eV. Subvalent doping by Al on the Sn site is energetically favourable and is proposed to be an efficient way to increase the Li content in Li2SnO3. The electronic structure calculations show that the introduction of Al will not introduce levels in the band gap

A comparative cross-reactivity and paraspecific neutralization study on Hypnale hypnale, Echis carinatus, and Daboia russelii monovalent and therapeutic polyvalent anti-venoms

Envenoming by the hump-nosed pit viper (Hypnale hypnale) raises concern as it inflicts significant debilitation and death in the Western Ghats of India and in the adjacent island nation of Sri Lanka. In India, its medical significance was realized only during 2007 due to its mis-identification as Echis carinatus and sometimes as Daboia russelii. Of late, several case reports have underlined the ineptness of the existing polyvalent anti-venom therapy against H. hypnale envenoming. Currently, H. hypnale bite has remained dreadful in India due to the lack of neutralizing anti-venom therapy. Hence, this study was undertaken to establish a systematic comparative, biochemical, pathological, and immunological properties of Sri Lankan H. hypnale venom alongside Indian E. carinatus, and D. russelii venoms. All three venoms differed markedly in the extent of biochemical activities including proteolytic, deoxyribonuclease, L-amino acid oxidase, 5'-nucleotidase, hyaluronidase, and indirect hemolytic activities. The venoms also differed markedly in their pathological properties such as edema, hemorrhage, myotoxic, cardiotoxic, and coagulant activities. The venoms showed stark differences in their protein banding pattern. Strikingly, the affinity-purified rabbit monovalent anti-venoms prepared against H. hypnale, E. carinatus, and D. russeliivenoms readily reacted and neutralized the biochemical and pathological properties of their respective venoms, but they insignificantly cross-reacted with, and thus failed to show paraspecific neutralization of any of the effects of the other two venoms, demonstrating the large degree of variations between these venoms. Further, the Indian therapeutic polyvalent anti-venoms from VINS Bioproducts, and Bharath Serums and Vaccines failed to protect H. hypnale venom-induced lethal effects in mice

A new series of 1,3,4-oxadiazole linked quinolinyl-pyrazole/isoxazole derivatives: synthesis and biological activity evaluation

A series of 1,3,4-oxadiazole bridged pyrazole/isoxazole bearing quinoline derivatives has been designed and synthesized by a clean and convenient method. Structures of the newly synthesized compounds have been confirmed by FTIR, H-1 and C-13 NMR, and HRMS spectral data. The titled compounds have been evaluated for their molecular docking guided antimicrobial and anti-inflammatory activity. One of 1,3,4-oxadiazole bridged quinolinyl-pyrazole derivatives has interacted efficiently with E. Coli protein (PDB file: 1KZN), and has been characterized by good antimicrobial activity against the majority of the tested pathogens. Another product has exhibited excellent anti-inflammatory activity

Influence of the Fly Ash Material Inoculants on the Tensile and Impact Characteristics of the Aluminum AA 5083/7.5SiC Composites

The choice of suitable inoculants in the grain refinement process and subsequent enhancement of the characteristics of the composites developed is an important materials research topic, having wide scope. In this regard, the present work is aimed at finding the appropriate composition and size of fly ash as inoculants for grain refinement of the aluminum AA 5083 composites. Fly ash particles, which are by products of the combustion process in thermal power plants, contributing to the large-scale pollution and landfills can be effectively utilized as inoculants and interatomic lubricants in the composite matrix–reinforcement subspaces synthesized in the inert atmosphere using ultrasonic assisted stir casting setup. Thus, the work involves the study of the influence of percentage and size of the fly ash dispersions on the tensile and impact strength characteristics of the aluminum AA 5083/7.5SiC composites. The C type of fly ash with the particle size in the series of 40–75 µm, 76–100 µm, and 101–125 µm and weight % in the series of 0.5, 1, 1.5, 2, and 2.5 are selected for the work. The influence of fly ash as distinct material inoculants for the grain refinement has worked out well with the increase in the ultimate tensile strength, yield strength, and impact strength of the composites, with the fly ash as material inoculants up to 2 wt. % beyond which the tensile and impact characteristics decrease due to the micro coring and segregation. This is evident from the microstructural observations for the composite specimens. Moreover, the role of fly ash as material inoculants is distinctly identified with the X-Ray Diffraction (XRD) for the phase and grain growth epitaxy and the Energy Dispersive Spectroscopy (EDS) for analyzing the characteristic X-Rays of the fly ash particles as inoculant agents in the energy spectrum

Melatonin restores neutrophil functions and prevents apoptosis amid dysfunctional glutathione redox system

Melatonin is a chronobiotic hormone, which can regulate human diseases like cancer, atherosclerosis, respiratory disorders, and microbial infections by regulating redox system. Melatonin exhibits innate immunomodulation by communicating with immune system and influencing neutrophils to fight infections and inflammation. However, sustaining redox homeostasis and reactive oxygen species (ROS) generation in neutrophils are critical during chemotaxis, oxidative burst, phagocytosis, and neutrophil extracellular trap (NET) formation. Therefore, endogenous antioxidant glutathione (GSH) redox cycle is highly vital in regulating neutrophil functions. Reduced intracellular GSH levels and glutathione reductase (GR) activity in the neutrophils during clinical conditions like autoimmune disorders, neurological disorders, diabetes, and microbial infections lead to dysfunctional neutrophils. Therefore, we hypothesized that redox modulators like melatonin can protect neutrophil health and functions under GSH and GR activity-deficient conditions. We demonstrate the dual role of melatonin, wherein it protects neutrophils from oxidative stress-induced apoptosis by reducing ROS generation; in contrast, it restores neutrophil functions like phagocytosis, degranulation, and NETosis in GSH and GR activity-deficient neutrophils by regulating ROS levels both in vitro and in vivo. Melatonin mitigates LPS-induced neutrophil dysfunctions by rejuvenating GSH redox system, specifically GR activity by acting as a parallel redox system. Our results indicate that melatonin could be a potential auxiliary therapy to treat immune dysfunction and microbial infections, including virus, under chronic disease conditions by restoring neutrophil functions. Further, melatonin could be a promising immune system booster to fight unprecedented pandemics like the current COVID-19. However, further studies are indispensable to address the clinical usage of melatonin