Ubiquitin-specific protease 14 (USP14) is a member of the Deubiquitinating enzymes (DUBs) involved in disrupting the regulation of the ubiquitin-proteasome system, responsible for the degradation of impaired and misfolded proteins which is an essential mechanism in eukaryotic cells. The involvement of USP14 in cancer progression and neurodegenerative disorders has been reported. Thereof USP14 is a prime therapeutic target; hence, designing efficacious inhibitors of USP14 is central in curbing these conditions. Herein, we relied on structural bioinformatics methods incorporating molecular docking, Molecular Mechanics Generalized Born Surface Area (MM-GBSA), Molecular dynamics simulation (MD simulation) and ADME to identify potential allosteric USP14 inhibitors. A library of over 733 compounds from the PubChem repository with >90% match to the IU1 chemical structure was screened in a multi-step framework to attain prospective drug-like inhibitors. Two potential lead compounds (CID 43013232 and CID 112370349) were shown to record better binding affinity compared to IU1, but with subtle difference to IU1-47, a 10-fold potent compound when compared to IU1. The stability of the lead molecules complexed with USP14 was studied via MD simulations. The molecules were found to be stable within the binding site throughout the 50ns simulation time. Moreover, the protein-ligand interactions across the simulation run time suggest Phe331, Tyr476, and Gln197 as crucial residues for USP14 inhibition. Furthermore, in silico pharmacological evaluation revealed the lead compounds as pharmacological sound molecules. Overall, the methods deployed in this study revealed two novel candidates that may show selective inhibitory activity against USP14, which could be exploited to produce potent and harmless USP14 inhibitors.

Molecular dynamics(MD) simulations are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals the solvent structure and preferential interaction sites (hot spots) on the protein surface. This information is largely transferable across all classes of protein ligands (from water to drugs) and can be used very effectively to understand ligand recognition and improve the predictive capability of well-established methods such as molecular docking. MD simulations for protein and drug or drug-like compounds are now being used but are still computationally expensive and can only be applied to specific cases. On the other hand, MDmix simulations can now be used in SBDD and we will describe the latest developments and implementations. We expect to see an increase in the application of these techniques to a plethora of protein targets to identify new drug candidates with the advent of new tools and faster computers.

Histone Lysine Specific Demethylase 1 (LSD1) is overexpressed in many cancers and become a new target for anticancer drugs. In recent years, the small molecule inhibitors with various structures targeting LSD1 have been reported. Here we report the binding interaction modes of a series of thieno[3,2-b]pyrrole-5-carboxamides LSD1 inhibitors using molecular docking, three dimensional quantitative structure-activity relationship (3D-QSAR). Comparative molecular field analysis (CoMFA q²=0.783, r²=0.944, r²_pred=0.851) and Comparative molecular similarity indices analysis (CoMSIA q²=0.728, r²=0.982, r²_pred=0.814) were used to establish 3D-QSAR models, which had good verification and prediction capabilities. Based on the contour maps and the information of molecular docking, 8 novel small molecules were designed in silico, among which compounds D4, D5 and D8 with high predictive activity were subjected to further molecular dynamics simulations (MD), and their possible binding modes were explored. It was found that Asn535 plays a crucial role in stabilizing the inhibitors. Furthermore, the ADME and bioavailability prediction for D4, D5 and D8 were carried out. The results would provide valuable guidance for designing new reversible LSD1 inhibitors in the future.

The use of New-age (Nano) Modified Emulsions (NME) for the stabilisation of marginal materials for use in the upper-pavement layers of roads have been proven in laboratories, through Accelerated Pavement Tests (APT) and in practice. In addition, material design methods have been developed based on the scientific analysis of granular material mineralogy and the chemical interaction with the binder to design a material compatible NME stabilising agent for naturally available (often marginal) materials. However, the introduction of any new disruptive technology in a traditionally well-established industry, such as the road construction industry, is usually associated with considerable resistance. This is especially relevant when the new technology enables the use of granular materials traditionally considered to be of an unacceptable quality in combination with relatively new concepts such as New-age (Nano) Modified Emulsions (NME). In practice, few road construction projects are without any problems. The introduction of new-technologies obviously makes it an easy target to blame for any non-related problem that may arise during construction. This article aims to assist in pre-empting, recognising, preventing and resolving material or non-material related construction problems through the correct identification of the cause of the problem and recommending the best, most cost-effective way to correct any deficiencies on site.

Preventing the occurrence of secondary caries serves as one of the significant issues in dental clinic, thus make it indispensable to improving the properties of conventional composite resin (CR) by developing a novel CR. In present study, two groups of experimental CRs loaded with different contents of fluoride-doped nano-zirconia fillers (25 wt% and 50 wt%) were fabricated. The surface topography, mechanical performance, fluoride release, antibacterial effect, aging property and cytotoxicity of the experimental CRs were evaluated subsequently. A uniform distribution of the F-zirconia fillers over the whole surface of resin matrix could be observed. The experimental CRs showed continuous fluoride release within 28 days, which was positively correlated with the content of F-zirconia fillers. Moreover, the amount of fluoride release increased in the acidic buffer. Addition of F-zirconia fillers could improve the color stability, wear resistance and microhardness of the experimental CRs, without reducing the flexure strength. Furtherly, the fluoride ions released continuously from the experimental CRs resulted in effective contact and antibacterial properties, while they showed no cytotoxicity. As a consequence, considerations can be made to employ this new kind of composite resin loaded with fluoride-doped nano-zirconia fillers to meet clinical requirements when the antimicrobial benefits are desired.

The application of dry lubrication in rolling contacts is challenging due to wear. In previous studies graphene platelets applied as dry lubricants on the surfaces of angular contact ball bearings demonstrated superior properties. These specific bearings, experiencing both rolling and spinning motion, create more severe conditions for dry lubricants. The applied graphene platelets have a thickness of few graphene layers in the nm range and a diameter in the µm range. Such platelets can be produced by mechanical exfoliation from graphite. To delve deeper into the lubrication effects, investigations were carried out using a milli tribometer. In the tests, a fixed steel ball is sliding against an oscillating counterpart under defined load. During the measurements, the applied load and tangential forces on the ball are recorded to calculate the friction. In our case, a steel ball with a diameter of 6 mm was used against graphene-based films on flat bearing surfaces (axial bearing washer). Comparative investigations included nano graphite particles and fullerene as dry lubricants, in addition to graphene platelets of various staple thicknesses. To increase the adhesion of the films to the surfaces, a pre-rolling process was implemented. Afterwards, the friction on the compressed films was measured. The results indicate that the pre-rolling process effectively reduces the friction of the system. After testing, the surfaces underwent analysis using laser scanning microscopy to assess the formed films, wear, and material transfer. It has been demonstrated that the pre-rolling process leads to the formation of a very thin compacted film with surface protective properties. On the ball as counterpart, the graphene platelets generate a transfer film on the contacting surface.

Soil salinity is seen as a major restriction for crop production, and with water scarcity this problem becomes more complicated. Mulching is crucial to salinity dynamics management by decreasing evaporation with improving the soil’s characteristics. Using chitosan as an eco-friendly biostimulant can enhance plant defense genes during different abiotic stresses. Recently, agricultural research has recognized nanoparticles as a pioneer material due to their distinctive physicochemical features. Therefore, a lysimeter experiment was conducted to investigate the interactive effects of mulching (UNM: un-mulched, WPM: white plastic, RSM: rice straw and SDM: sawdust) and chitosan foliar application (Ch0: control, Ch1: 250 mg chitosan L-1, Ch2: 125 mg nano chitosan L-1, and Ch3: 62.5 mg nano chitosan L-1) on the biochemical soil characteristics and common beans productivity under salt affected soil conditions. Organic mulching (RSM and SDM) treatments significantly improved the soil's organic carbon, available nutrient content, and total count of bacteria. WPM treatment lowered soil EC to 6.63 dS m-1 and increased soil water content to 34.13%. The application of Ch3 caused considerable increases in the plant height, shoot dry weight, root dry weight, grain yield, and nutrient content in the seed. The total fungi count in the soil and Na% in the seed was significantly decreased due to chitosan foliar applications. Moreover, the interactive effect of different mulch materials plus foliar by chitosan applications gave a statistically similar seed yield in both seasons. Overall, this study revealed the potential of the mulching treatments and foliar application of nano chitosan in improved biochemical soil characteristics and common bean productivity under saline soil conditions.

In this paper we introduce the concept of Nano Beta Closure, Nano Beta Interior and study the relationship between them also study some of their properties. Based on these notions we introduced the topological Approach to Decision Making and Its Application in the Medical Field" which describes the use of topological methods in decision-making, specifically through the utilization of nano beta closure and nano beta interior. These mathematical tools are applied in the medical field to improve diagnostic accuracy and aid in treatment planning. The authors demonstrate the effectiveness of this approach through a case study on the diagnosis of Chronic Kidney. The results show that the topological approach using nano beta closure and nano beta interior provides a reliable and accurate method for medical decision-making. Finally, we introduce a medical application for disease groups patients of with chronic kidney. To identify the main causative agent of kidney disease. where using this approach, the medical team can identify the specific areas of the kidney that are affected by the infection, as well as the extent of damage and any potential complications. This information is used to create an individualized treatment strategy that is customized to meet the specific requirements of the patient. and medical history. We write an algorithm that can be a helpful tool for doctors to utilize in diagnosing infection disease Chronic Kidney infections. By utilizing this approach, clinicians can provide accurate diagnoses, develop effective treatment plans, and ultimately improve patient outcomes. finally, we show that fractals hold significant importance in future nano topological generation of the human factor. Their unique properties and self-similar patterns offer insights into the complex organization of biological systems and provide a foundation for designing advanced Nanosystems.

Diabetes mellitus is a cluster of metabolic diseases characterized by hyperglycemia. Since this epidemic growing worldwide, the usage of phototherapeutics to manage diabetes is vital. Coccinia grandis (Aka ivy gourd) belongs to cucumber family is identified as a most effective herb, especially for diabetes and many other disease conditions. Hence, an instant herbal porridge cube incorporating Coccinia grandis leaf powder was produced and sensory acceptability of the porridge was evaluated using trained panelists. The bioactive activity of Coccinia grandis leaf powder showed that 66.77±0.74 mg/g GAE of Total Phenolic Content, 27.65±6.79% of DPPH radical scavenging activity, 5.72% of alpha-amylase inhibition activity and 59.64% of alpha-glucosidase inhibition activity. The effect on postprandial blood sugar levels after consuming the developed porridge was measured using healthy adults and it was observed there was no blood sugar elevation during the 2 hours of time. As a further development, Coccinia grandis leaf extract was nano-encapsulated with food grade Sodium alginate and it was incorporated into the same porridge as a safe delivery method of bioactive compounds. In-vitro digestion assay was conducted and the results show that alpha-amylase inhibition activity for the gastric phase and alpha-glucosidase inhibition activity for the intestinal phase was higher in nano-encapsulated porridge. The study concludes that, consuming nano-encapsulated Coccinia grandis leaf extract with porridge is more beneficial for diabetic patients.

Organophilic nano clay is the composition of mostly clay and organic molecules designed to improve various materials' physical and chemical properties. Permanent deformation in asphalt pavements is primarily the result of inadequate compaction, excessive loading, and high temperatures. Rutting can result in aquaplaning, leading to accidents and costly maintenance and rehabilitation works that drain the economy. Such behavior of asphalt pavements may be attributable to poor selection of aggregate, asphalt binder, or substandard asphalt binders. This study used different percentages of organophilic nano clay ranging from 3.0% - 5.0% with two penetration grade bitumen, i.e., N.R.L 60-70 & N.R.L 80-100. Adding organophilic nano clay to asphalt binder significantly reduced the rutting potential under cyclic loading at high temperatures (55 °C). Ten modified formulations and two virgin bitumen specimens were prepared. The modified binders' viscosity and rutting were tested using the Rotational Viscometer and Wheel Tracker Test (W.T.T.), respectively. The results were analyzed using software for Statistical Analysis. It was recorded that organophilic nano clay-modified bitumen significantly affected rutting to interpret the results. The results indicated that rutting decreased and viscosity increased in all nano clay-modified bitumen samples, with a 4.5% O.N.C modified binder showing the most significant improvement.

The present work is focused on functionalizing Montmorillonite (Mt) with poly dimethyl siloxane (PDMS) to develop a hybrid membrane reactor for the removal of Co (II) and Ni (II) ions from model wastewater samples. The specific surface area of the novel material was found to be 444 m2 /g. X-Ray Diffraction (XRD) and Fourier Transform Infra-Red (FTIR) spectra reveal the formation of exfoliated composite material. The efficiency of this membrane material was determined by subjecting it to continuous filtration experiments. It was able to remove 50% of Co (II) and 75% of Ni (II) ions, respectively, in one cycle of filtration in less than three minutes of operation with a permeate flux rate of 675 L/m2/H and 975 L/m2/H respectively, for both the ions.

This work presents the production and incorporation of calcium hydrolyzed nano-solutions at three concentrations (1, 2, and 3 wt.%) in alkali-activated gold mine tailings (MTs) from Arequipa, Perú. A first activator solution of sodium hydroxide (NaOH) at 10M was used. The calcium hy-drolyzed nano-solutions acted as a secondary activator and as additional calcium resource for the alkali-activated materials (AAMs) based on the low-calcium gold MTs. High-resolution trans-mission electron microscopy/energy-dispersive x-ray spectroscopy (HR-TEM/EDS) analyses were carried out to characterize the morphology, size, and structures of the calcium hydrolyzed na-noparticles. Fourier transform infrared (FTIR) analyses then were used to understand the chemical bonding interactions in the calcium hydrolyzed nanoparticles and in the AAMs. Scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDS) and Quantitative X-ray diffraction (QXRD) were performed to study the structural, chemical, and phase compositions of the AAMs; uniaxial compressive tests evaluated the compressive strength of the reacted AAMs; and Nitrogen adsorption-desorption analyses measured the porosity changes at nanostructure level in the AAMs. The results indicate that each increase in the concentration of the calcium hydrolyzed nano-solution had a direct/proportional effect on the mechanical properties of the AAMs samples. The AAMs with 3 wt.% calcium-hydrolyzed nano-solution had the highest compressive strength value of 15.16 MPa, which represented an increase of 62% compared to the original system without nanoparticles and aged under the same conditions of 70°C for seven days. These results provide useful information about the positive effect of calcium-hydrolyzed nanoparticles on gold MTs and their conversion into sustainable building materials through alkali activation.

Of course, now we know that quantum mechanics has been a fundamental structure of our world since our universe came into being. However, it has been only a century since the experimental and theoretical discovery of quantum mechanics and its extensions into many implications and applications. In particular, there are implications across many disciplines that most likely will affect education, health, security, etc. Examples are given of the need for starting education as early as possible in schools, the use of nano-robots to deliver drugs targeted to specific molecular sites, to developing new cryptographic systems to safeguard our privacy.

The size of TiO2 (either nanometric or micrometric) can significantly affect both its photocatalytic and photoelectrochemical properties, thus altering the photooxidation of organic pollutants in air or water. The purpose of this work is to give an account of the photoelectrochemical and photocatalytic features of some nano- and micro-sized TiO2 commercial powders towards a model reaction, the photooxidation of acetone. Cyclic voltammograms (CV) of TiO2 particulated electrodes under UV illumination experiments were carried out in either saturated O2 or N2 solutions for a direct correlation with the photocatalytic process. In addition, the effect of different reaction conditions on the photocatalytic efficiency under UV light in both aqueous and gaseous phases was also investigated. CV curves with the addition of acetone under UV light showed a negative shift of the photocurrent onset, confirming the efficient transfer of photoproduced reactive oxygen species (ROSs), e.g., hydroxyl radicals, or holes to acetone molecules. The photocatalytic experiments showed that the two nano-sized samples exhibit the best photocatalytic performance. The different photoactivity of the micro-sized samples is probably attributed to their morphological differences, affecting both the amount and distribution of free ROSs involved in the photooxidation reaction.

Amorphous ferrite-type rare-earth (RE) substituted garnets and garnet-oxide nanocomposite layers are prepared on clear glass substrates by using RF magnetron sputter-deposition process. By using a combination approach employing custom-built spectrum-fitting software in conjunction with Swanepoel’s envelope method, the spectral dispersion function of optical constants and the layer thicknesses are derived accurately from the transmission spectra of the as-deposited samples. The effects of excess metal-oxides added to the base material systems during the co-deposition process are found to affect the refractive index and the optical absorption coefficients of garnet-oxide composites. A number of optical constant datasets are presented, enabling the experimentalists to design nanophotonic or integrated-optics devices employing these functional materials.

Aiming at the damage detection and continuous monitoring of high efficiency composite structure, the method of carbon nano sensor embeded in the 3-D braided composite material specimen was put forward and the method of damage location for 3-D braided composite material was described. In this paper, the mechanical and electrical characteristics of carbon nano-fiber were analyzed. Considering the massive data of the health monitoring of composite processing, to ensure that the system has good real-time performance, quaternary matrix Singular Value Decomposition algorithm is proposed to simplify data and improve the efficiency of the algorithm. The existence of injury is determined and the damage location is calculated by comparing with key features of healthy specimen. Experimental results prove the method is feasible and effective.

A new class of nano-cube core-shell heterostructures containing Ag coating on the top of WO₃ was fabricated. Physical vapor deposition was used to produce WO₃ based nano-heterostructures. All kind of wet toxic chemical process was avoided to make the process simple and contaminant free. Sputtering of WO₃ and a subsequent thermal annealing process was done to create nano-cubes of WO₃. After that, sputtering of Ag was performed to form the Ag-WO₃ core-shell nano-heterostructures (CSNH). The CSNHs were characterized using field emission scanning electron microscopy (FESEM), energy dispersive spectroscopy (EDS), X-ray diffraction analysis (XRD) and UV-vis spectroscopy. The morphologies, elemental analysis, interfaces, crystallinity, phases, and chemical compositions were analyzed. The bottom-up growth of WO₃ nanocubes was studied using different time periods at 900°C. Ag coating was also studied before and after annealing. Finally, an optical property (band gap) was also analyzed using Tauc plot derive from absorption spectra. The tailoring the band gap of WO₃ from ~2.9eV to ~ 2.45 eV was observed while Ag-WO₃ CSNH formed.

The growing interest in Kv7.2/7.3 agonists originates from the involvement of these channels in several brain hyperexcitability disorders. In particular, Kv7.2/7.3 mutants have been clearly associated with epileptic encephalopathies (DEE) as well as with a spectrum of focal epilepsy disorders, often associated with developmental plateauing or regression. Nevertheless, there is a lack of available therapeutic options, considering that retigabine, the only molecule used in clinic as broad-spectrum Kv7 agonist, has been withdrawn from the market in the late 2016. This is why several efforts have been made both by both academia and industry in the search for suitable chemotypes acting as Kv7.2/7.3 agonists. In this context, in silico methods have played a major role, since the precise structures of different Kv7 homotetramers have been only recently disclosed. In the present review the computational methods used for the design of Kv.7.2/7.3 small molecule agonists and the underlying medicinal chemistry are discussed in the context of their biological and structure-function properties.

Innovations in drug delivery systems are crucial for enhancing therapeutic efficiency. Our research presents a novel approach based on Electro-fluid dynamic atomization (EFDA) to fabricate core-shell monophasic particles (CSMp) from sodium alginate blends of varying molecular weights. This study explores the morphological characteristics of these particles in relation to material properties and process conditions, highlighting their potential in drug delivery applications. A key aspect of our work is the development of a mathematical model that simulates the release kinetics of small molecules, specifically sodium diclofenac. By assessing the diffusion properties of different molecules and gel formulations through transport and rheological models, we have created a predictive tool for evaluating the efficiency of these particles in drug delivery. Our findings underscore two critical independent parameters for optimizing drug release: the external shell thickness and the diffusivity ratios within the dual layers. This allows for precise control over the timing and intensity of the release profile. The study advances our understanding of EFDA in the fabrication of CSMp and offers promising avenues for enhancing drug delivery systems by tailoring release profiles through particle characteristic manipulation.

The type III receptor tyrosine kinase FLT3 is a pivotal kinase for hematopoietic progenitor cell regulation, with significant implications in acute myeloid leukemia (AML) through mutations like internal tandem duplication (ITD). This study delves into the structural intricacies of FLT3, the roles of activation loop mutants, and their interaction with tyrosine kinase inhibitors. Coupled with this, the research leverages molecular contrastive learning and protein language modeling to examine interactions between small molecule inhibitors and FLT3 activation loop mutants. Utilizing the ConPLex platform, over 5.7 million unique FLT3 activation loop mutants-small molecule pairs were analyzed. The binding free energies of three inhibitors were assessed, and cellular apoptotic responses were evaluated under drug treatments. Notably, the introduction of the Xepto50 scoring system provides a nuanced metric for drug efficacy. The findings underscore the modulation of molecular interactions and cellular responses by Y842 mutations in FLT3-KD, highlighting the need for tailored therapeutic approaches in FLT3-ITD-related malignancies.

The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral Integrase (IN) enzyme catalyses integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG) and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of Integrase Strand Transfer Inhibitors (INSTIs). In this study, we applied computational methods of molecular modelling and docking to analyse the effect of NOPs on the full-length IN structure and INSTI binding. We identified 16 NOPs within the Cameroonian derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any effect on INSTI binding. INSTIs displayed similar binding affinities to each IN structure. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment naïve populations. This study supports the use of second-generation INSTI DTG as part of first-line combination antiretroviral therapy (cART) regimens, due to DTG possessing a stronger genetic barrier to the emergence of drug resistance.

The increasingly common occurrence of antibiotic-resistant bacteria has become an urgent public health issue. There are currently some infections without any effective treatment, which require new therapeutic strategies. An attractive alternative is the design of compounds capable of disrupting bacterial communication known as quorum sensing (QS). In gram-negative bacteria, such communication is regulated by acyl-homoserine lactones (AHLs). QS allows bacteria to proliferate before expressing virulence factors. Our group previously reported that hexyloxy phenyl imidazoline (9) demonstrated 71% inhibitory activity of QS at 100 µM (IC50=90.9 µM) in Chomobacterium violaceum, a gram-negative bacterium. The aim of the present study was to take 9 as a lead compound to design and synthesize three 2-imidazolines (13-15) and three 2-oxazolines (16-18), to be evaluated as quorum sensing inhibitors on C. violaceum CV026. We were looking for compounds with a higher affinity towards the Cvi receptor of this bacterium and the ability to inhibit QS. The binding mode of the test compounds on the Cvi receptor was explored with docking studies and molecular dynamics. It was found that 8-pentyloxyphenyl-2-imidazoline 13 reduced the production of violacein (IC50=56.38 µM) without affecting bacterial growth, suggesting inhibition of quorum sensing. Indeed, compound 13 is apparently one of the best QS inhibitors known to date. Molecular docking revealed the affinity of compound 13 for the orthosteric site of the N-hexanoyl homoserine lactone (C₆-AHL) on the CviR protein. Ten aminoacid residues in the active site of C₆-AHL interacted with 13, and 7 of these are the same as those interacting with AHL. Contrarily, 8-octyloxyphenyl-2-imidazoline 14, 8-decyloxyphenyl-2-imidazoline 15 and 9-decyloxyphenyl-2-oxazoline 18 bound only to an allosteric site and thus did not compete with C₆-AHL for the orthosteric site.

Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative and antineoplastic activities. Recently, different studies have shown that flavonoid have the potential to inhibit BET bromodomains. Previous reports suggest that flavonoids are putative inhibitors of the ZA channel due to their orientation and interactions with P86, V87, L92, L94 and N140. Herein, a comprehensive characterization of the binding mode of the biflavonoid amentoflavone and fisetin is discussed. To this end, both compounds were docked with BRD4 using four docking programs. Results were post-processed with protein-ligand interaction fingerprints. To gain further insights into the binding mode of the two natural products, docking results were further analyzed with molecular dynamics. Results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as basis for scaffold optimization and further characterization of flavonoids as BET inhibitors.

Caveolin-1 (Cav-1) is 22 kDa caveolae protein, acts as a scaffold within caveolar membranes. It interacts with alpha subunits of G-protein and thereby regulates their activity. Earlier studies reported elevated or up-regulated levels of caveolin-1 in the serum of prostate cancer patients. Secreted Cav-1 promotes angiogenesis, cell proliferation and anti-apoptotic activities in prostate cancer patients. Cav-1 upregulation is mainly related to prostate cancer metastasis. Keeping above facts in view, the present study was designed to explore Cav-1 as a target for prostate cancer therapy using computational approach. Molecular docking, structural base molecular modelling and molecular dynamics simulations were performed to investigate Cav-1 inhibitors. A predictive model was generated and validated to establish a stable structure. ZINC database of biogenic compounds was used for induced fit docking (IFD) and high throughput virtual screening. The H-bond interactions of the compounds with active site residues of Cav-1 were estimated by IFD and 100 ns long molecular dynamic simulations. The reported compounds showed significant binding and thus can be considered as potent therapeutic inhibitors of Cav-1. This study provides a valuable insight into biochemical interactions of Cav-1 for therapeutic applications and warrants for experimental validation of the predicted ‘active(s)’.

The bipartite entanglement is comprehensively investigated in the mononuclear molecular complex (Et3NH)[Ni(hfac)2L], where HL denotes 2-(2-hydroxy-3-methoxy-5-nitrophenyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-3-oxide-1-oxyl and hfacH stands for hexafluoroacetylacetone. From the magnetic point of view, the molecular compound (Et3NH)[Ni(hfac)2L] consists of an exchange-coupled spin-1 Ni2+ magnetic ion and a spin-12 nitronyl-nitroxide radical substituted nitrophenol. The nickel-radical molecular complex affords an experimental realization of a mixed spin-(12, 1) Heisenberg dimer with a strong antiferromagnetic exchange coupling J/kB= 505 K and two distinct g-factors gRad=2.005 and gNi=2.275. By adopting this set of magnetic parameters we demonstrate that the Zeeman splitting of a quantum ferrimagnetic ground-state doublet due to a weak magnetic field may substantially reinforce the strength of bipartite entanglement at low temperatures. The molecular compound (Et3NH)[Ni(hfac)2L] maintains sufficiently strong thermal entanglement even at room temperature, vanishing only above 546 K. Specifically, the thermal entanglement in the nickel-radical molecular complex retains approximately 40% of the maximum value corresponding to perfectly entangled Bell states at room temperature, which implies that this magnetic compound provides suitable platform of a molecular qubit with potential implications for room-temperature quantum computation and quantum information processing.

Drug nanosuspensions offer a promising approach to improve bioavailability for poorly soluble drug candidates. Such formulations often necessitate the inclusion of an excipient to stabilize the drug nanoparticles. However, a rationale to choose the correct excipient for a given drug candidate remains unclear. To gain molecular insight into formulation design, this work first utilizes molecular dynamics simulation to computationally investigate drug-excipient interactions for a number of combinations that have been previously studied experimentally. We find that hydrophobic interactions drive excipient adsorption to drug nanoparticles, and that the fraction of polar surface area serves as a predictor for experimental measurements of nanosuspension stability. To test these ideas prospectively, we applied our model to an uncharacterized drug compound, GDC-0810. Our simulations predicted that salt forms of GDC-0810 would lead to more stable nanosuspensions than the neutral form; therefore, we tested the stability of salt GDC-0810 nanosuspensions and found that the salt form readily formed nanosuspensions even without excipient. To avoid computationally expensive simulations in the future, we extended our model by showing that simple, two-dimensional properties of the single drug molecule can be used to rationalize nanosuspension design without simulation. In all, our work demonstrates how computational tools can provide molecular insight into drug-excipient interactions, and aid in rational formulation design.

We extend a previously developed model for the Stark resonances of the water molecule. The method employs a partial-wave expansion of the single-particle orbitals using spherical harmonics. To find the resonance positions and decay rates, we use the exterior complex scaling approach which involves the analytic continuation of the radial variable into the complex plane and yields a non-hermitian Hamiltonian matrix. The real part of the eigenvalues provides the resonance positions (and thus the Stark shifts), while the imaginary parts $-\Gamma/2$ are related to the decay rates $\Gamma$, i.e., the full-widths at half-maximum of the Breit-Wigner resonances. We focus on the three outermost (valence) orbitals, as they are dominating the ionization process. We find that for forces directed along the three Cartesian co-ordinates, the fastest ionizing orbital always displays a non-monotonic Stark shift. For the case of fields along the molecular axis we show results as a function of the number of spherical harmonics included ($\ell_{\max}=3,4$). Comparison is made with total molecule resonance parameters from the literature obtained with Hartree-Fock and coupled cluster methods.

Biological membranes are fascinating. Santiago Ramón y Cajal, who received the Nobel prize in 1906 together with Camillo Golgi for their work on the nervous system, wrote “[..]in the study of this membrane[..] I felt more profoundly than in any other subject of study the shuddering sensation of the unfathomable mystery of life”[1]. The visualization and conceptualization of these biological objects have profoundly shaped many aspects of modern biology, drawing inspiration from experiments, computer simulations, as well as from the imagination of scientists and artists. The aim of this review is to provide a fresh look on current ideas of biological membrane organization and dynamics by discussing selected examples across fields [1] The full quotation is “I must not conceal the fact that in the study of this membrane I for the first time felt my faith in Darwinism (hypothesis of natural selection) weakened, being amazed and confounded by the supreme constructive ingenuity revealed not only in the retina and in the dioptric apparatus of the vertebrates but even in the meanest insect eye. There, in fine, I felt more profoundly than in any other subject of study the shuddering sensation of the unfathomable mystery of life.” from the autobiography Recollections of My Life.

It’s been reported that Mori Folium (MF) and Eucommiae Cortex (EC) exhibit pharmacological effects on the treatment of immunosuppression. However, the mechanism of MF and EC against immunosuppression remains unclear. This study aims to explore the mechanism of action of MF and EC for the treatment of immunosuppression through network pharmacology, molecular docking, molecular dynamics simulations and animal experiments. As a result, 11 critical components, 9 hub targets, and related-signaling pathways of treatment of immunosuppression were obtained based on network pharmacology. The molecular docking suggested that 11 critical components exhibited great binding affinity to 9 hub targets of immunosuppression. The molecular dynamics simulations results showed that (-)-Tabernemontanine-AR, beta-sitosterol-AR and Dehydrodieugenol-HSP90AA1 complexes are stably bound. Additionally, in the animal experiments, the treated group results compared to the control group suggest that MF and EC have a significant effect on the treatment of immunosuppression. Therefore, the MF and EC treatment for immunosuppression may take effects in a multi-component, multi-target, and multi-pathway manner. The results would provide novel insights into the treatment of immunosuppression in humans.

Organic-organic interactions play important roles in the secondary organic aerosol formation, but the interactions are complex and poorly understood. Here we use environmental molecular beam experiments combined with molecular dynamics simulations to investigate the interactions between methanol and nopinone, as atmospheric organic proxies. In the experiments, methanol monomers and clusters are sent to collide with three types of surfaces, i.e., graphite, thin nopinone coating on graphite and multilayer surfaces, at temperatures between 140 K and 230 K. Methanol monomers are efficiently scattered from the graphite surface, whereas the scattering is substantially suppressed from nopinone surfaces. The desorption from the three surfaces is similar, suggesting that all the surfaces have weak or similar influences on the methanol desorption. The molecular dynamics results show that upon collisions the methanol clusters shatter, and the shattered fragments quickly diffuse and recombine to clusters. The desorption involves a series of processes, including detaching from clusters and desorbing as monomers. The experimental results also show that all trapped methanol molecules completely desorb within a short experimental time scale at temperatures of 180 K and above. At lower temperatures, the desorption rate decreases, and a long experimental time scale is used to resolve the desorption, where three desorption components are identified. The fast component is beyond the experimental detection limit. The intermediate component exhibits multi-step desorption character and has an activation energy of E_a = 0.18 ± 0.03 eV, in good agreement with simulation results. The slow desorption component is related to diffusion processes due to the weak temperature dependence.

Kidneys of mice, rats and humans possess progenitors that maintain daily homeostasis and take part in endogenous regenerative processes following injury, owing to their capacity to proliferate and differentiate. In the glomerular and tubular compartments of the nephron, consistent studies demonstrated that well-characterized, distinct populations of progenitor cells, localized in the parietal epithelium of Bowman capsule and scattered in the proximal and distal tubules, could generate segment-specific cells in physiological conditions and following tissue injury. However, defective or abnormal regenerative responses of these progenitors can contribute to pathologic conditions. The molecular characteristics of renal progenitors have been extensively studied, revealing that numerous classical and evolutionarily conserved pathways, such as Notch or Wnt/β-catenin, play a major role in cell regulation. Others, such as retinoic acid, renin-angiotensin-aldosterone system, TLR2 (Toll-Like Receptor 2) and leptin, are also important in this process. In this review, we summarize the plethora of molecular mechanisms directing renal progenitor responses during homeostasis and following kidney injury. Finally, we will explore how single cell RNA sequencing could bring the characterization of renal progenitors to the next level, while knowing their molecular signature is gaining relevance in the clinic.

Aquaporin-3 (AQP3) is one of the aquaglyceroporins, which is expressed in the basolateral layer of the skin membrane. Studies have reported that human skin squamous cell carcinoma overexpresses AQP3 and inhibition of its function may alleviate skin tumorigenesis. In the present study, we have applied a virtual screening method that encompasses filters for physicochemical properties and molecular docking to select potential hit compounds that bind to the Aquaporin-3 protein. Based on molecular docking results, the top 20 hit compounds were analyzed for stability in the binding pocket using unconstrained molecular dynamics simulations and further evaluated for binding free energy. Furthermore, examined the ligand-unbinding pathway of the inhibitor from its bound form to explore possible routes for inhibitor approach to the ligand-binding site. With a good docking score, stability in the binding pocket, and free energy of binding, these hit compounds can be developed as Aquaporin-3 inhibitors in the near future.

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM, and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound, and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

Micro nano bubbles (MNBs) can generate ·OH in situ, which provides a new idea for the safe and efficient removal of pollutants in water supply systems. However, the difficulty in obtaining stable MNBs causes the low efficiency of ·OH generation, which makes the inability to guarantee the removal efficiency of pollutants. This paper reviews the application research of MNBs technology in water security from three aspects: the generation process of MNBs in water, the generation rule of ·OH during MNBs collapse, and the control mechanism of MNBs on pollutants and biofilms. We found that MNBs generation methods are divided into chemical and mechanical (about 10 kinds) categories, and the instability of bubble size restricts the application of MNBs technology. The generation of ·OH by MNBs is affected by pH, gas source, bubble size, temperature, external stimulation. And pH and external stimulus have more influence on ·OH generation in situ than other factors. Adjusting pH to alkaline or acidic conditions and selecting ozone or oxygen as the gas source can promote the ·OH generation. MNBs’ collapse also releases a large amount of energy, which the temperature and pressure can reach 3000K and 5Gpa respectively, making it efficient to remove ≈90 % of pollutants (i.e., trichloroethylene, benzene, and chlorobenzene). The biofilm can also be removed by physical, chemical, and thermal effect. MNBs technology also has great application potential in drinking water, which can be applied to improve water quality, optimize household water purifiers, and enhance the taste of bottled water. Under the premise of safety, let people of different ages taste, finding that compared with ordinary drinking water, 85.7 % of people think MNBs water is softer, 73.3 % of people think MNBs water is sweeter. This further proves that MNBs water has a great prospect in the drinking water application. This review provides innovative theoretical support for solving the problem of drinking water safety.

Protein–nanoparticle hybridization can ideally lead to novel biological entities characterized by emerging properties, which can sensibly differ from those of the parent components. Herein, the effect of ionic strength on the biological functions of recombinant, His-tagged spermine oxidase (i.e., SMOX) was studied for the first time. Moreover, SMOX was integrated to colloidal surface active maghemite nanoparticles (SAMNs) by direct self-assembly, leading to a biologically active nano-enzyme (i.e., SAMN@SMOX). The hybrid was subjected to an in-depth chemical-physical characterization highlighting that protein structure was perfectly preserved. The catalytic activity of the nanostructured hybrid (SAMN@SMOX) was assessed by extracting kinetics parameters using spermine as substrate and compared to the soluble enzyme as a function of ionic strength. Results revealed that the catalytic function was dominated by electrostatic interactions and that they were drastically modified upon hybridization with colloidal ɣ-Fe2O3. Noteworthy, the affinity of SMOX toward spermine was significantly higher for the nanohybrid at low salinity. The present study supports the vision of using protein–nanoparticle conjugation as a mean for modulating biological functions.

Significant amount of oil remains in the reservoir after primary and secondary operations and to recover the remaining oil, enhanced oil recovery (EOR) can be applied as one of the feasible options remaining nowadays. In this study new nano polymeric materials have been prepared from purple yam and cassava starches. The yield of purple yam nanoparticles (PYNPs) was 85% and that of cassava nanoparticles (CSNPs) is 90.53%. Synthesized materials were characterized through particle size distribution (PSA), zeta potential distribution, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). The performance of PYNPs in recovering oil was better than CSNPs as found from recovery experiments. Zeta potential distribution results confirmed the stability of PYNPs over CSNPs (-36.3 mV for PYNPs and -10.7 mV for CSNPs). The optimum concentration for these nanoparticles has been found from interfacial tension measurements and rheological properties and it was 0.60 wt.% for PYNPs and 0.80 wt.% for CSNPs. More incremental recovery (33.46%) has achieved for the polymer that contained PYNPs in comparison to the other nano-polymer (31.3%). This opens the inception for a new technology for polymer flooding that may replace the conventional method that depends on partially hydrolyzed polyacrylamide (HPAM).

We synthesized iron(II)-triazole spin crossover compounds of the type [Fe(atrz)3]X2 and incorporated and deposited them on electrospun polymer nanofibers. In view of possible applications, we chose iron(II)-triazole-complexes that are known to exhibit spin crossover close to ambient temperature. Therefore we used the complexes [Fe(atrz)3]Cl2 and [Fe(atrz)3](2ns)2 (2ns = 2Naphthalenesulfonate) and analyzed them with IR-, UV/Vis and Mossbauer spectroscopy and with a SQUID magnetometer. The synthesized complexes were then in one attempt deposited on fibers of polymethylmethacrylate (PMMA) and in another attempt incorporated into core-shell like PMMA fiber structures. This was done via two different electrospinning methods. Deposition was performed by uniaxial electrospinning and incorporation was performed by coaxial electrospinning. The obtained polymer-complex-composites were then further investitgated by the same methods as the pure complexes as well as by SEM pictures and EDX measurements. The analysis by UV/Vis spectroscopy, Mössbauer spectroscopy and temperature-depended magnetic measurements with the SQUID magnetometer showed that the spin crossover properties were maintained and were not changed after the electrospinning processes and that the complexes were not harmed during the procedure.

The physicalchemistry properties and crystal structure of were nano-ZrO₂+3mol.%Y₂O₃ determined. The kinetics of the formation of H₂ as a result of the decomposition of H₂O on the surface of nano-ZrO₂+3mol.%Y₂O₃ was studied. Effects of adsorption and desorption process on ZrO₂+3 mol.%Y₂O₃ nanoparticles were studied at different (T=400÷1000⁰C) temperature. The study of H₂ in thermal processes at nano-ZrO₂+3 mol.%Y₂O₃ system increased. Such an increase in H₂ generation in comparison with a pure H₂O as thermal processes had formedactive centers for H₂O decomposition on the surface of the catalyst at the expense of δ-electrons emitted on the surface of nano-ZrO₂+3 mol.%Y₂O₃. This showed that the dimensions of the studied nanoscale particles systems are comparable to the free running distance of energy carriers generated by of nano-ZrO₂+3 mol.%Y₂O₃ as a result of thermal processes. These results are promising for hydrogen generation by waer spliting in near future.

This paper seeks to optimize the mechanical and durability properties of ultra-high performance concrete (UHPC). To meet this objective, concrete specimens were manufactured by using 1,100 kg/m3 of binder, water/binder ratio 0.20, silica sand and last generation of superplasticizer. Silica fume, metakaolin and two types of nano silica were used for improving the performances of the concrete. Additional mixtures included 13mm long OL steel fibers. Compressive strength, electrical resistivity, mercury intrusion porosimetry tests and differential and thermogravimetric thermal analysis were carried out. The binary combination of nano silica and metakaolin, and the ternary combination of nano silica with metakaolin and silica fume, led to the best performances of the UHPC, both mechanical and durable performances.

We fabricated the nano-aperture plasmonic platforms for single molecule detection and other various applications such as infrared thermal emission device. The nano-apertures including the nanopores on the pyramid, and the nano-slits on the Au flat membrane were fabricated using a Ga ion focused ion beam drilling technique, followed by high energy electron beam irradiations dependent upon the electron beam current density. The nanopores with a few nanometer size and the nanoslit array with order of ~ 100 nm width were fabricated. Optical characteristics for the various nanoslits were examined dependent upon the slit opening width and sample thickness. The broad emission spectra from the (7x 7) slit array are obtained from spp-mediated emission in the visible and infrared region. A sharp strong infrared emission peak is also obtained due to Au nanoparticle. The fabricated Au platform can be utilized as single molecule sensor and infrared thermal emission device.

The awareness of the existence in plants of bioactive compounds namely phytochemicals (PHYs), having health properties is progressively expanding. Therefore, their massive introduction in the normal diet, in food supplements, and their use as natural therapeutics to treat several diseases are increasingly emphasized by several sectors. Particularly, most PHYs possessing antifungal, antiviral, anti-inflammatory, antibacterial, antiulcer, anti-cholesterol, hypoglycemic, immunomodulatory, and antioxidant properties have been isolated from plants. Additionally, their secondary modification with new functionalities, to further improve their intrinsic beneficial effects, is extensively investigated. Unfortunately, although the idea of exploiting PHYs as therapeutics is amazing, its realization is far from simple, and the possibility of exploiting them as effective orally administrable drugs is almost utopic. Most PHYs are insoluble in water and, when introduced orally, they scarcely reach the site of action in therapeutic concentrations. Degradation by enzymatic and microbial digestion, occurring in the mouth, stomach, and intestine, as well as fast metabolism and rapid excretion via the kidney, biliary, or lung, strongly limit their in vivo activity. To overcome these drawbacks, several nanotechnological approaches have been used and many PHYs-loaded delivery systems with dimensions of nanometers have been developed. This paper, also by reporting various recent case studies, reviews the foremost nano-suspension and nano-emulsion-based techniques developed for formulating the most relevant PHYs in more bioavailable nanoparticles (NPs), suitable or promising for clinical application. Also, the acute and chronic toxic effects due to the exposure to NPs reported so far, the possible nanotoxicity which could derive by their massive employment, as well as the ongoing actions to improve the knowledge in the field were discussed. The state of the art concerning the actual clinical application of both PHYs and the nanotechnologically engineered PHYs was also reviewed.

The novel coronavirus disease 19 (COVID-19) has resulted in an estimated 20 million excess deaths and the recent resurgence of COVID-19 in China is predicted to result in up to 1 million deaths over the next few months. With vaccines unable to halt transmission it is important to continue our quest for safe, effective, affordable drugs that will be available to all countries. Drug repurposing is one of the strategies being explored in this context. Recently, out of 7,817 approved drugs, 214 candidates were systematically down-selected using a combination of 11 filters including approval status, assay data against SARS-CoV-2, pharmacokinetic, pharmacodynamic and toxicity profiles. These drugs were subjected in this study to virtual screening against various targets of SARS-CoV-2 followed by molecular dynamic studies of the best scoring ligands against each target. The chosen molecular targets were Spike receptor binding domain, Nucleocapsid protein RNA binding domain, and key non-structural proteins 3, 5, 12, 13 and 14. Four drugs approved for other indications — alendronate, cromolyn, natamycin and treprostinil — look sufficiently promising from our in silicostudies to warrant further in vitro and in vivo investigations as appropriate to ascertain their extent of anti-viral activities.

The monkeypox virus (MPXV) has become a major threat due to the increasing global caseload and the ongoing multi-country outbreak in non-endemic territories. Due to limited research in this avenue and the lack of intervention strategies, the present study was aimed to virtually screen bioactive phytochemicals against envelope proteins of MPXV via rigorous computational approaches. Molecular docking and molecular dynamic (MD) simulations were used to investigate the binding affinity of 12 phytochemicals against three envelope proteins of MPXV, viz., D13, A26, and H3. Silibinin, oleanolic acid, and ursolic acid were computationally identified as potential phytochemicals that showed strong binding affinity towards all the tested structural proteins of MPXV through molecular docking. The stability of the docked complexes was also confirmed by MD simulations. ADME analysis also computationally confirmed the drug-like properties of the phytochemicals, thereby asserting their suitability for consumption. Hence, this study envisions the candidature of bioactive phytochemicals as promising inhibitors against the MPXV, serving as template molecules that could further be experimentally evaluated for their efficacy against monkeypox.

Zika virus (ZIKV) has been characterized as one of the potential pathogens and placed under future epidemic outbreaks by the WHO. However, lack of potential therapeutics can result in uncontrolled pandemic like other human pandemic viruses; therefore, prioritized effective therapeutics development has been recommended against ZIKV. In this context, the present study adopted the strategy to explore the lead compounds from Azadirachta indica against ZIKV via concurrent inhibition of the ZIKVpro and ZIKVRdRp proteins using molecular simulations. Initially, structure-based virtual screening of 44 bioflavonoids reported in Azadirachta indica against the crystal structures of targeted ZIKV proteins resulted in the identification of top four common bioflavonoids, viz. rutin, nicotiflorin, isoquercitrin, and hyperoside. These compounds showed substantial docking energy (-7.9 to -11.01 kcal/mol) and intermolecular interactions with essential residues of ZIKVpro (His51, Asp74, and Ser135) and ZIKVRdRp (Asp540, Ile799, and Asp665) by comparison to the reference compounds, O7N inhibitor (ZIKVpro) and Sofosbuvir inhibitor (ZIKVRdRp). Long interval molecular dynamics simulation (500 ns) on the selected docked poses reveals the stability of respective docked complexes contributed by intermolecular hydrogen bonds and hydrophobic interactions. The predicted complex stability was further supported by calculated end-point binding free energy using molecular mechanics generalized born surface area (MM/GBSA) method. Consequently, the identified common bioflavonoids are recommended as promising therapeutic inhibitors of ZIKVpro and ZIKVRdRp for further experimental assessment.

An important stage in SARS-CoV-2 life cycle is the fusion of spike(S) protein with the ACE2 host-cell receptor. Therefore, to explore conserved features in S protein dynamics and to identify potentially novel regions for drugging, we measured variability derived from 791 viral genomes and studied its properties by MD simulation. The findings indicated that S2 subunit (HR1, CH, and CD domains) showed low variability, low fluctuations in MD, and displayed a trimer cavity. By contrast, the RBD domain, which is typically targeted in drug discovery programmes, exhibits more sequence variability and flexibility. Interpretations from MD suggest that the monomer is in constant motion showing transitions up-to-down state, and the trimer cavity may function as a 'bouncing spring' that may facilitates S protein interactions with ACE2. Feasibility of trimer cavity for potential drug target was examined by SBVS screening. Several hits that have already been validated or suggested to inhibit the SARS-CoV-2 virus in cell systems were identified; in particular, the data suggest an action mechanism for such molecules including Chitosan and macrolide types. These findings identify a novel binding-site formed by the S protein, that might assist in future drug discovery programmes aimed at targeting the CoV family of viruses.

The global pandemic caused by the new SARS-COV-2 coronavirus makes it necessary to search for drugs for its control. Within of this research it has been known that the ivermectin drug, a FDA-approved drugs which is formulated as an 80:20 mixture of ivermectin B1a and B1b and used commonly for parasitic infections, has an inhibitory effect on viruses, includes SARS-COV-2 at in vitro level. In the particular case of SARS-COV-2 its mechanism of action remains elusive and controversial. Interestingly, the energy of interaction of ivermectin with any of the proteins the SARS-CoV-2 and the possible structural alterations at the protein level that this drug can cause have not been reported. In this sense, we carried out a bioinformatics study with docking strategies and molecular dynamics to predict the binding and disturbance induced by ivermectin in proteins associated with SARS-CoV-2. We use DockThor and Molegro docking scores. The DockThor server and myPresto software were used to build complexes and dynamics studies, respectively. The results obtained suggested that ivermectin is capable of docking with the 3CL protease and the HR2 domain, and may promote structural changes in these proteins by inducing unfolding/folding. Specifically, ivermectin brings protease to a significantly more deployed conformational state and the HR2 domain to a more compact state compared to the native state. Finally, it is shown that B1a and B1b macrocyclic lactones have a behavior different from to each target protein. These results suggest a possible inhibitory effect against SARS-CoV-2 due to a synergistic role of this drug to spontaneously bind to two important proteins involve in the proliferation of this virus. However, more studies are required on this possible mechanism of action.

The SARS-CoV-2 was confirmed to cause the regional outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. The 3C-like protease (3CL^pro), an essential enzyme for viral replication, is a valid target to compacts SARS-CoV and MERS-CoV. In this research, an integrated library consisting of 1000 compounds from Asinex Focused Covalent (AFCL) library and 16 FDA-approved protease inhibitors were screened against SARS-CoV-2 3CL^pro. Top compounds with significant docking scores and making stable interactions with catalytic dyad residues were obtained. The screening results in identification of compound 621 from AFCL library as well as Paritaprevir and Simeprevir from FDA-approved protease inhibitors as potential inhibitors of SARS-CoV-2 3CL^pro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CL^pro were characterized using 50 nanoseconds (ns) molecular dynamic (MD) simulation approach. The identified compounds are potential inhibitors worthy of further development as SARS-CoV-2 3CLpro inhibitors/drugs. Importantly, the identified FDA-approved therapeutics could be ready for clinical trials to treat infected patients and help to curb the COVID-19.

The antioxidant activity of molecules constitutes an important factor for the regulation of redox homeostasis and reduction of oxidative stress. Cells affected by oxidative stress can undergo genetic alteration, causing structural changes and promoting the onset of chronic diseases, such as cancer. The in silico study performed here was developed to evaluate the antioxidant potential of two molecules, ZINC08706191 (Z91) and ZINC08992920 (Z20), with recognized epithelial anticancer potential. Molecular docking, chemical-quantum calculations and Pearson's correlation were performed. The Z91 and Z20 molecules showed lower binding free energy (ΔG) values for the receptor-ligand interaction than the reference molecules (caffeine – CAF and ascorbic acid – AA), and better results for values of molecular descriptors correlated with ΔG, resulting in a decrease of ΔG. Strong correlations were observed between ΔG values for the five receptors evaluated and ΔG values of the potential epithelial anticancer activity available in literature. These results attest to the significant antioxidant potential of the Z91 and Z20 molecules and their strong relation with the potential epithelial anticancer activity and may be indicated for further analysis in relation to the control of oxidative stress and epithelial anticancer activity.

Borneol and menthol were two terpenes wildly used as penetrate enhancer in transdermal drug delivery. To explore their penetration enhancement effect towards hydrophilic drug, 5-FU was selected as model drug. A method combined vitro permeation studies and coarse grain molecular dynamics was used to investigate their penetration enhancement effect towards 5-FU. As a result, although both borneol and menthol showed a penetration enhancement effect towards 5-FU, they differed a lot in the penetration enhancement mechanism, which was also thought to account for their different penetration enhancement effect. As for menthol, SC bilayer disrupting effect seemed to be its main mechanism. While for borneol, its mechanism seemed to be more complicated. Except for disrupting the SC bilayer, it could also increase the permeation of 5-FU by enhancing the diffusion rate of 5-FU or inducing the formation of transient pore. All of this enable us a molecular understanding of borneol and menthol’s penetration enhancement effect towards hydrophilic drug, which might provide some guidance in the latter research and application.

Recently perovskite solar cells have been paying attention of researchers. This comes from their high efficiency and stability. In this work, the change of some Optical and Electrical Properties of BaxFe(1-x)TiO4 thin films due to the change of the nanocrystal spacing and size were studied. A simple theoretical model based on the string theory was utilized to explain some of these empirical relations. The empirical results obtained indicated that an increase in the efficiency of the nano solar cell requires the energy gap to be narrow. Decreasing the nanocrystal size and spacing caused the energy gap to become narrower. The energy gap decreases also upon increasing the absorption coefficient and decreasing the transmission. This also requires increasing the conductivity and the magnetic permeability. The increase of the nanocrystal spacing decreases the absorption coefficient, electrical conductivity, and magnetic permeability, while it causes the transmission to increase. All these changes are explained using a simple string model beside Newton's laws. The capability of the string theory to explain this Nano quantum behavior comes from the fact that the string theory, like quantum theory, recognizes both the particle and the wave nature of the Nano system.

Oral bone defects occur as a result of trauma, cancer, infections, periodontal diseases, and caries. Autogenic and allogenic grafts are the gold standard used to treat and regenerate damaged or defective bone segments. However, these materials do not possess the antimicrobial properties necessary to inhibit the invasion of the numerous deleterious pathogens present in the oral microbiota. In the present study poly(ε-caprolactone) (PCL), nano-hydroxyapatite (nHAp), and a commercial extract of Humulus lupulus L. (hops) were electrospun into polymeric matrices to assess their po-tential for drug delivery and bone regeneration. The fabricated matrices were analyzed by scanning electron microscopy (SEM), tensile analysis, thermogravimetric analysis (TGA), FT-IR assay, and in vitro hydrolytic degradation. The antimi-crobial properties were evaluated against the oral pathogens Streptococcus mutans, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans. The cytocompatibility was proved by the MTT assay. SEM analysis proved the nanostructured matrices have suitable fiber size. The present research provides new information about the interaction of natural compounds with ceramic and polymeric biomaterials. The hop extract and other natural or synthetic medicinal agents can be effectively loaded into PCL fibers and has the potential to be used in biomedical applications.

In this study, sodium alginate (SA) was oxidized with potassium periodate to produce an alginate-based tanning agent. Using OSA as a biodegradable tanning agent and a nano-hydroxyapatite (nano-HAp) low concentration suspension to give flame retardancy to leather, eco-design concepts were applied to establish a chrome-, aldehyde-, and phenol-free tanning process. Micro-DSC, 1H NMR, attenuated total reflection mode Fourier transform infrared spectroscopy (FTIR-ATR), and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS) were used to investigate the complex matrix collagen-OSA-nano-HAp. Micro-differential scanning calorimetry (micro-DSC) was used to assess OSA's ability to interact with collagen and stabilize the collagen-OSA matrix, while 1H unilateral nuclear magnetic resonance (NMR) was used to investigate the aqueous environment and limitations around collagen molecules caused by their association with OSA and nano-HAp. Industrial standard tests were used to assess mechanical properties and fire resistance of the new leather prototype. The findings reported here indicate that both OSA and nano-HAp are suitable alternatives for cleaner tanning technologies and more sustainable leather.

In recent years, frequent occurrences of low temperature disasters due to global climate change have significantly impacted the normal growth of crops. Research has indicated that inorganic selenium (which is more toxic) can not only enhance the effects of low temperature stress but also increase selenium content on plants; however, there is a scarcity of studies investigating the impacts of organic selenium and nano-selenium on crops. In order to investigate whether organic selenium and nano-selenium can enhance low-temperature tolerance and increase selenium content in pak choi (Brassica chinensis var. pekinensis. cv. ‘Suzhouqing’), different concentrations (0, 5, 10, 20 mg L-1) of exogenous selenium were applied in this experiment to assess their effects on plant growth, nutritional quality and antioxidant properties. RNA-Seq technology was used to sequence the transcriptome of the leaves. Based on the transcriptome data, a Weighted Gene Co-expression Network Analysis (WGCNA) was employed to construct a network that associates with physiological traits related to stress resistance. Two highly correlated gene co-expression modules were identified, and within them, nine hub genes associated with endocytosis, antioxidant stress, absorption, transport, and metabolism of selenium were discovered. The results indicated that the beneficial effects on yield and total selenium content under low temperature were attributed to (1) protection of photosynthetic pigments for enhancing photosynthetic capacity by the up-regulation of LHca2, LHcb1, LHca1, LHcb4 in KEGG pathway: photosynthesis-antenna proteins; (2) activation of antioxidant system for efficient ROS homeostasis such as SOD, POD and CAT by the genes such as Superoxide dismutase, Monodehydroascorbate and (3) selenium absorption by endocytosis, seleninum transportation by ABC transporter gene family and selenium metabolism related genes such as Cysteine synthase, Glutaredoxin. These findings provide a foundation for further investigation into the molecular mechanisms underlying the effects of organic selenium and nano-selenium on cyanochloride production at low temperatures.

The creation of nano-zero-valent iron (nZVI) by implementing plant extracts is an environmentally friendly process. High antioxidant capacity and phenol content indicated the possibility of oak-nZVI synthesis using oak leaf extract as a stable material with minimal agglomeration. Simultaneously removal of Cd and phosphates and Ni and phosphates was optimized by a statistically designed experiment with a definitive screening design. In terms of significance, 4 input parameters on process productivity were monitored: initial metal concentration (1 - 9 mgL-1), initial ion concentration (1- 9 mgL-1), pH value (2 - 10) and oak-nZVI dosage (2 - 16 ml). Phosphate removal efficiency, in the presence of cadmium, was the most influenced by oak-nZVI dose and cadmium concentration, while pH gave three statistically significant interactions with oak-nZVI dosage, cadmium concentration, and phosphate concentration. Phosphate removal efficiency, in the presence of Ni, is the most influenced by nickel concentration, phosphate concentration, pH, two-factor interaction between nZVI dose and Ni concentration, and quadratic phosphate interaction. The process optimization yielded the highest simultaneous removal efficiency of 98.99% and 87.30% for cadmium and phosphate ions, respectively. Also, the highest simultaneous removal efficiency of nickel and phosphates ion was 93.44% for 96.75%, respectively. The optimization process fits into the confidence intervals, confirming the assumption that the adopted regression model describes the process well. This work demonstrated an enormous potential and prosperous application for the Cd(II), Ni(II), and phosphate removal from water matrices.

Using analysis methods such as Rutherford backscattering Spectrometry, scanning electron microscopy, X-ray diffraction, and Raman spectroscopy, the diffusion behavior of iodine in micro/nano-porous graphite under high-temperature conditions was studied. The results indicate that iodine diffusion leads to the contraction of graphite microcrystals, a decrease in interlayer spacing, and an increase in defect density, resulting in a reduction in microcrystal size. Upon diffusion of iodine out of iodine-loaded graphite, the microcrystal size of the graphite increases, the interlayer spacing appears to return to the initial state, and the defect density decreases. By comparing the iodine diffusion performance of nanoporous graphite G400 and G450 with microporous graphite G500, it was determined that nanoporous graphite exhibits better inhibition of iodine diffusion compared to microporous graphite. Studying the diffusion behavior of iodine in micro/nano-porous graphite has significant academic significance and engineering value for the screening, design, and performance optimization of nuclear graphite.

In this work the effect of recycled concrete aggregate modified with mineral admixtures and Nano-silica on the mechanical properties and performance of the concrete was investigated after curing in tap water for 28 and 90 days. The compressive, ƒc, indirect tensile, ƒt, and flexural, ƒb, strengths for cured concrete specimens were measured and concrete strength ratios were analyzed. The water and rapid chloride permeability were measured. SEM analysis of microstructure was, also, investigated. The coarse aggregates used were dolomite (control) and recycled concrete aggregate with the incorporation of different mineral admixtures including ground granulated blast slag and granite as well as Nano-silica. It was found that, the slump values of the dolomite concrete decreases compared with recycle aggregate concrete. The results indicate that, the concrete mix containing recycle aggregate have the highest compressive strength, tensile strength and flexural strength compered to concrete mix containing dolomite aggregate. As far as the compressive strength is concerned, the addition 1 % NS and 15 % of slag improved the physico-mechanical properties of the recycled aggregate concretes compared to the other mixes after curing in tap water.

Tissue engineering and regenerative medicine has gradually evolved as a promising therapeutic strategy to the modern healthcare of the aging and diseased population. In this study, we developed a novel nano-fibrous scaffold and verified its application in the critical bone defect regeneration. The metformin-incorporated nano-gelatin/hydroxyapatite fibers (NGF) was produced by electrospinning, cross-linked, and then characterized by XRD and FTIR. Cytotoxicity, cells adhesion, cell differentiation, and quantitative osteogenic gene and protein expression were analyzed by bone marrow stem cells from rat. Rat forearm critical bone defect model was performed for the in vivo study. The nano-gelatin/hydroxyapatite fibers (NGF) were characterized by their porous structures with proper interconnectivity without significant cytotoxic effects; the adhesion of bone marrow stem cells on the nano-gelatin/hydroxyapatite fibers (NGF) could be enhanced. The osteogenic gene and protein expression were upregulated. Post implantation, the new regenerated bone in bone defect was well demonstrated in the NGF samples. We demonstrated that the metformin-incorporated nano-gelatin-hydroxyapatite fibers greatly improved healing potential on the critical sized bone defect. Although metformin-incorporated nano-gelatin/hydroxyapatite fibers had advantageous effectiveness during bone regeneration, further validation is required before it can be applied to clinical applications.

Phytophthora. infestans is a well known late blight causing oomycetes pathogen. It evolves and adapts to the host background and new fungicide molecules rapidly within a few years of their release, may be due to the predominance of transposable elements in its genome. Frequent and huge applications of fungicides cause environmental concerns. Here we developed target specific RNA interference based molecules, that are capable of effectively reducing the late blight infection. cDNA microarray expression data was used for the selection of genes involved in the early stage of infection process, sporulation etc. The in vitro synthesis of double stranded RNA molecule, targeting SDH, EF-1α, GPI-HAM344, PLD-3 and HSP-90 encoding genes revealed the reduction in growth, sporulation and symptom expression, which were subsequently assessed by culture bioassay, detached leaf assay and topical application methods. The multiple genes targeted dsRNA nano clay sprayed plants showed enhanced disease resistance (4% disease severity) and least sporulation (<1x103), compared to naked dsRNA spray. Use of nano clay was assumed to be involved in the effective delivery, protection and boosting the action of RNAi in potato plants. A significant difference in the growth, sporulation count, disease severity and reduced expression of the genes and confocal microscopy imaging authenticates the effects of SIGS on late blight disease progression. Our research demonstrated that topical dsRNA nano clay spray under the open-air environment could be an alternative to chemical fungicides and transgenic approaches as a novel plant protection strategy for late blight in an environmentally friendly manner.

Currently, metal nanoparticles have varied uses for different medical, pharmaceutical, and agricultural applications. Nano-biotechnology combined with green chemistry has great potential for the development of novel and necessary products that benefit human activities, while encourages the reduction of hazardous reagents for nanoparticle production. Green chemistry has an important role due to its contribution to unconventional synthesis methods of gold and silver nanoparticles from plant extracts, which have exhibited antimicrobial potential among other outstanding properties. Biodiversity-rich countries need to collect and convert knowledge from biological resources into processes, compounds, methods, and tools, which need to be achieved along with sustainable use and exploitation of biological diversity. Therefore, this review focuses on the importance of metal nanoparticles, the use of plant extract for their synthesis as well as other available methods, and the relevant antimicrobial activity that can be exploited in a sustainable model of agricultural management through a modern nanotechnological approach.

Porosity in plasma sprayed coatings is vital for most engineering applications. It is either advantageous or disadvantageous depending on the functionality of the coating and the immediate working environment. Consequently, the formation mechanisms and development of porosity has been extensively explored to find out modes of controlling porosity in plasma sprayed coatings. In this work, a comprehensive review of porosity on plasma sprayed coatings is established. The formation and development of porosity on plasma sprayed coatings are governed by set spraying parameters. Optimized set spraying parameters have been used to achieve the most favorable coatings with minimum defects. Even with the optimized set spraying parameters, defects like porosity still occur. Here, we discuss other ways that can be used to control porosity in plasma sprayed coating with emphasis to atmospheric plasma sprayed chromium oxide coatings. Techniques like multi-layer coatings, nano-structured coatings, doping with rare earth elements, laser surface re-melting and a combination of the above methods have been suggested in adjusting porosity. The influences of porosity on properties of plasma sprayed coatings and the measurement methods of porosity have also been reviewed.

Traditional silicon binary circuits continue to face challenges such as high leakage power dissipation and large area of interconnections. Multiple-Valued Logic (MVL) and nano-devices are two feasible solutions to overcome these problems. In this paper, we present a novel method to design ternary logic circuits based on Carbon Nanotube Field Effect Transistors (CNFETs). The proposed designs use the unique properties of CNFETs, e.g., adjusting the Carbon Nanotube (CNT) diameters to have the desired threshold voltage and have the same mobility of P-FET and N-FET transistors. Each of our designed logic circuits implements a logic function and its complementary via a control signal. Also, these circuits have a high impedance state which saves power while the circuits are not in use. We show a more detailed application of our approach by designing a two-digit adder-subtractor circuit. We simulate the proposed ternary circuits using HSPICE via standard 32nm CNFET technology. The simulation results indicate the correct operation of the designs under different process, voltage and temperature (PVT) variations. Moreover, we designed a two-digit adder/subtractor and a power efficient ternary logic ALU based on the proposed gates. Simulation results show that the two-digit adder/subtractor using our proposed gates has 12X and 5X lower power consumption and PDP (power delay product) respectively, compared to previous designs.

Metal and alloy toughening was the core and long-term research direction in materials filed. As grain size had bimodal distribution, micro/nano-structured alloys presented excellent comprehensive mechanical properties, and this had become one of the research hotspots and developing trends in the field of nanotechnology. In-situ tensile test was a direct and effective method to study the deformation mechanism of materials, which revealed the multiple mechanisms responding to feature grain sizes and provided reliable experimental means and research technique. Research on development of in-situ technique and its applications in mechanical properties was reviewed in this paper according to the recent advances on the modern mechanical properties for high strength and high plasticity alloy at home and abroad. The disadvantages of the present study of preparation methods and investigation techniques for high-performance alloy had been concluded. Finally, the development prospects of high strength and high plasticity alloy materials were analyzed.

Benzazoles, such as benzoxazoles and benzothiazoles, are compounds with important biological and pharmacological activities and important intermediaries in synthesis. This report presents a linear synthesis of a butanamide derived from linking 5-chloro-2-aminobenzoxazole and 2-aminobenzothiazole via 4-chlorobutanoyl chloride. The corresponding compound N-(benzothiazol-2-yl)-4-((5-chlorobenzoxazol-2-yl)aminobutanamide was obtained in good [PVG1] yield using accessible starting materials and methodology in two reaction steps. Furthermore, we made docking studies of this compound on 3-TOP protein to explore its potential as an antidiabetic agent with an excellent yield.

Interferons were the original prototype cytokine system discovered in 20th-century research. As the name implies, they were originally thought to be synthesised and secreted between cells. Thanks to technological advances, the processes involved in protein secretion can be explained comparatively more clearly at both the genetic and biochemical levels. The discovery of interferon (IFN) occurred when genetic research was still in its infancy. Franklin and Wilkins discovered the structure and function of deoxyribonucleic acid (DNA) at the same time as Crick and Watson; however, Isaacs and Lindemann, two scientists, described the first IFN in 1957. Mutations can be caused by inherent genetic protein synthesis and during infection as well as within IFN regulation pathways affecting cell proliferation. This remains central to host cell IFN synthesis and effects through IFN protein receptor subunits defined by 6 protein domains. Type II IFN is key to immune cell function secreted by a variety of immune cells, mainly natural killer (NK) as well as T cells. Single–stranded and/or double–stranded RNA/DNA viruses, as well as bacterial infections (e.g., Escherichia coli) and fungal infections (e.g., Aspergillus), also affect IFN regulation. Pathogenic proteins utilise intra/extracellular proteins that sense foreign antigens like Toll–like Receptors (TLRs), affected by mutations within the human cellular IFN transduction pathways. Since the discovery of the third IFN type in 2003, when immune cell phenotypes were further characterised, questions remain about the immunological mechanisms contributing to the regulation of the innate and adaptive host immune system. Alterations in the synthesis of type I/II/III host IFNs can differentially and beneficially alter homeostatic cellular pathways in pathological disease, with type I IFN being synthesised in cancer as well as by homeostatic cells. Therefore, considered here are the overall IFN molecular, cell regulatory mechanisms in the context of immune cell research developments.

A self-consistent charge density-functional tight-binding method combined with molecular dynamics simulations is employed to reveal the effect of polymorph on the thermal decomposition stability of 1,1-Diamino-2,2-Dinitroethylene (FOX-7). Two types of heating, constant temperature heating and temperature-programmed heating, are adopted. Potential evolution indicates that γ-FOX-7 possesses the lowest thermal stability, as it is closer to the decomposition state. Crystal form has an important influence on the thermal decomposition of FOX-7, resulting in different decomposition rates and initial reactions. In general, β- and γ-FOX-7 always decompose more completely than α-FOX-7. This work emphases the importance of polymorph dependent initial decay of an energetic polymorphic compound once heated in a volume constrained condition.

CoFe2O4 is a promissing catalytic material for many chemical reactions. We have used ab initio molecular dynamic simulations to study the structure and reactivity of the A- and B-terminations of the low index CoFe2O4 (001) surfaces to water adsorption at room temperature. Upon adsorption, water partly dissociates on both termination with a higher dissociation degree on the A- termination (30% versus 19%). The 2-fold coordinated Fe3+(tet) in the tetrahedral voids and the 5-fold coordinated Fe3+(oct) in the octahedral voids are the main active sites for water dissociation on the A- and B-termination, respectively. Molecular water, hydroxydes and surface OH resulting from proton transfer to surface oxygens are present on the surfaces. Both water free sur- face terminations undergo reconstruction. The outermost Fe3+(tet) on the A-termination and B-termination move towards the nearby unoccupied octahedral voids. In the presence of a thin film of 32 water molecules, the reconstructions are partially and completely lifted on the A- and B-termination, respectively.

We research the interaction between six representative carbon-based nanoparticles (CBNs) and 20 standard amino acids through all-atom molecular dynamics simulations. The six carbon-based nanoparticles are fullerene(C60), CNT55L3, CNT1010L3, CNT1515L3, CNT2020L3, and two-dimensional-graphene(Graphene33). Their curvatures decrease sequentially, and all of CNT are single-walled carbon nanotubes. We have observed that as the curvature of CBNs decreases, the adsorption effect of 20 amino acids with them has an increasing trend. In addition, we also used multi-dimensional clustering to analyze the adsorption effects of 20 amino acids on six carbon-based nanoparticles. We observed that the π-π interaction still plays an extremely important role in the adsorption of amino acids on carbon-based nanoparticles. Individual long-chain amino acids and “Benzene-like” Pro also have a strong adsorption effect with carbon-based nanoparticles.

Drug discovery has been initially attributed to coincidence or trial and error where the traditional approach was complex, lengthy, and expensive. Conventional drug discovery methods require the costly random screening of synthesized compounds or natural products. Another downside for this approach is the wide dependency on the experimental use of animals for in vi-vo testing. Currently, in silico modeling has become a vital tool for drug discovery and repurposing, and molecular docking is being used to find the best matching between a ligand and a molecule. Practical application of in silico docking will predict the biomolecular interactions between the drug and the target host. Beauvericin (BEA) is an emerging mycotoxin produced by the entomopathogenic fungus Beauveria bassiana. Originally investigated for its pesticide capability, BEA is now considered as a molecule of interest for its potentially diverse biotechnological applications in the pharmacological industry and the field of medicine. In this manuscript, we will provide an overview of the repurposing of BEA into a potentially superior therapeutic molecule in a broad range of diseases. Furthermore, considerable attention has been given to the fundamental role of in silico techniques to i) further investigate the spectrum of this secondary metabolite and ii) elucidate the pathways of BEA for its promising therapeutic action

Bioluminescence – i.e., the emission of visible light by living organisms - is defined as a biochemical reaction involving, at least, a luciferin substrate, an oxygen derivative, and a specialised luciferase enzyme. In some cases, the enzyme and the substrate are durably associated and form a photoprotein. While this terminology is educatively useful to explain bioluminescence, it gives a false idea that all luminous organisms are using identical or homologous molecular tools to achieve light emission. As usually observed in biology, reality is more complex. To date, 11 different luciferins have indeed been discovered, and several non-homologous luciferases lato sensu have been identified which, all together, confirms that bioluminescence emerged independently multiple times during the evolution of living organisms. While some phylogenetically related organisms may use non-homologous luciferases (e.g., at least four convergent luciferases are found in Pancrustacea), it has also been observed that phylogenetically distant organisms may use homologous luciferases (e.g., parallel evolution observed in some cnidarians, tunicates and echinoderms that are sharing a homologous luciferase-based system). The evolution of luciferases then appears puzzling. The present review takes stock of the diversity of known “bioluminescent proteins”, their evolution and potential evolutionary origins. A total of 134 luciferase and photoprotein sequences have been investigated (from 75 species and 11 phyla), and our analyses identified 12 distinct types – defined as a group of homologous bioluminescent proteins. The literature review indicated that genes coding for luciferases and photoproteins have potentially emerged as new genes or have been co-opted from ancestral non-luciferase/photoprotein genes. In this latter case, the homologous gene’s co-options may occur independently in phylogenetically distant organisms.

Li₂MnO₃ is critical component in the well-studied Li-excess cathode materials xLi₂MnO₃•(1- x)LiMO₂ for achieving high lithium storage capacity. In this article, the diffusion of Li ions in Li₂MnO₃ is studied using molecular dynamics (MD) simulation with well-behaved empirical force fields obtained by fitting against the crystal structure from experiment and phonons calculated using Density Function Theory (DFT). We have found two possible tetrahedral hopping channels, 0-TM and 1-TM(Mn⁴⁺) channel, which are differentiated by the face sharing octahedral cations. Simulation results show that the 0-TM channel is active for Li hopping, while 1-TM(Mn4+) channel is inactive. During the delithiation process, the Li ions in the TM layered are firstly removed, then those in the Li layer. However, the Li ions will be trapped in the tetrahedral 0-TM channels as long as the four face sharing octahedral sites are cleared. Up to x=1.0 for Li₂-xMnO₃, almost all the Li ions are located at the tetrahedral sites, forming a regular array along a axis. The de-intercalation of tetrahedral Li ions requires a high voltage (>5.2 V vs. Li/Li+), limiting the practical capacities measured in lab. The diffusion of Mn ions into the Li layers is observed in a deeper delithiated structure (x=1.2 for Li₂-xMnO₃), indicating an initial phase transformation to a spinel-like structure. However, the Mn ions are mainly trapped in the tetrahedral sites in the Li layer, instead of the octahedral sites fin spinel-like structure. A few of Mn ions diffusing into the octahedral sites in Li layers have no face sharing tetrahedral Li ions, revealing a further Li de-intercalation is imperative for the complete phase transformation. Our model is not stable for x≥1.4 in Li₂-xMnO₃. Other charge compensation mechanism should be considered in this high delithiation stage, eg. oxygen release.

An important parameter in the development of a new drug is the drug's affinity to the identified target (protein/enzyme). Predicting the ligand binding to the target (protein/enzyme) by molecular simulation would allow the synthesis to be restricted to the most promising compounds.A restricted hybrid HF-DFT calculation was performed in order to obtain the most stable conformer of each ligand and a series of DFT calculations using the B3LYP levels with 6-31G* basis set has been conducted. The docking studies of the quinolone compounds will be performed with the CLC Drug Discovery Workbench to identify and visualize the ligand-receptor interaction mode.

Introduction of exotic species in new areas through anthropic action is one of the major problems that can affect biodiversity. Branchiomma luctuosum is known for its highly invasive potential and the actual occurrence of species commonly associated with port activity areas is an extra evidence that this anthropogenic activity should not be underestimated. In order to develop suitable molecular markers for future studies on colonization routes and population dynamics of the invading individuals of B. luctuosum, nine highly polymorphic microsatellite loci were isolated and their polymorphism levels were evaluated. These loci showed a range of number of alleles per locus from five to ten and all loci had a high level of genetic diversity, and exhibited significant heterozygote deficiencies probably due to the presence of null alleles. Significant deviations from the Hardy-Weinberg equilibrium were detected at several loci and most of them were related to a heterozygous deficit. Heterozygous deficiency can be expected in this case due to the biology and history of this invasive species, in relation to its recent introduction in Brazilian coast and possible action of multiple introductory events.

Stabilization of a G-quadruplex (G4) in the promotor of the c-MYC proto-oncogene leads to inhibition of gene expression, and it thus represents a potentially attractive new strategy for cancer treatment. However, most G4 stabilizers show little selectivity among the many G4s present in the cellular complement of DNA and RNA. Intriguingly, a crescent-shaped cell-penetrating thiazole peptide, TH3, preferentially stabilizes the c-MYC G4 over other promotor G4s, but the mechanisms leading to this selective binding remain obscure. To investigate these mechanisms at the atomic level, we performed an in silico comparative investigation of the binding of TH3 and its analogue TH1 to the G4s from the promotors of c-MYC, c-KIT1, c-KIT2, and BCL2. Molecular docking and molecular dynamics simulations, combined with in-depth analyses of non-covalent interactions and bulk and per-nucleotide binding free energies, revealed that both TH3 and TH1 can induce the formation of a sandwich-like framework through stacking with both the top and bottom G-tetrads of the c-MYC G4 and the adjacent terminal capping nucleotides. This framework produces enhanced binding affinities for the c-MYC G4 relative to other promotor G4s, with TH3 exhibiting an outstanding binding priority. Van der Waals interactions were identified to be the key factor in complex formation in all cases. Collectively, our findings fully agree with available experimental data. Therefore, the identified mechanisms leading to specific binding of TH3 towards the c-MYC G4 provide valuable information to guide the development of new selective G4 stabilizers.

Tuberculosis (TB) continues to pose a global health challenge, exacerbated by the rise of drug-resistant strains. The development of new TB therapies is an arduous and time-consuming process. To expedite the discovery of effective treatments, computational structure-based drug re-purposing has emerged as a promising strategy. From this perspective, conditionally essential targets present a valuable opportunity, and the mycobactin biosynthesis pathway stands out as a prime example highlighting the intricate response of Mycobacterium tuberculosis (Mtb) to changes in iron availability. This study focuses on the re-purposing and revival of FDA-approved drugs (library) as potential inhibitors of MbtA, a crucial enzyme in mycobactin biosynthesis in Mtb conserved among all species of mycobacteria. Literature suggests this pathway to be associated with drug efflux pumps, which potentially contribute to drug resistance. This makes it a potential target for antitubercular drug discovery. Herein we utilized cheminformatics and structure-based drug repurposing approaches, viz., molecular docking, dynamics, and PCA analysis, to decode the intermolecular interactions and binding affinity of the FDA-reported molecules against MbtA. The virtual screening revealed ten molecules with significant binding affinities and interactions with MbtA. These drugs, originally designed for different therapeutic indications (4: antiviral, 3: anticancer, 1: CYP450 inhibitor, 1: ACE inhibitor, and 1: leukotriene antagonist), are repurposed as potential MbtA inhibitors. Furthermore, our study explores the binding modes and interactions between these drugs and MbtA, shedding light on the structural basis of their inhibitory potential. Principal component analysis highlighted significant motions in MbtA-bound ligands, emphasizing the stability of the top Protein-Ligand Complexes (PLCs). This computational approach provides a swift and cost-effective method for identifying new MbtA inhibitors, which can subsequently undergo validation through experimental assays. This streamlined process is facilitated by the fact that these compounds are already FDA-approved and have established safety and efficacy profiles. This study has the potential to lay the groundwork for addressing the urgent global health challenge at hand, specifically in the context of combating Antimicrobial Resistance (AMR) and Tuberculosis (TB).

Polo-like kinase 1 (PLK1) plays a pivotal role in cell division regulation and emerges as a promising therapeutic target for cancer treatment. Consequently, the development of small-molecule inhibitors targeting PLK1 has become a focal point in contemporary research. The adenosine triphosphate (ATP)-binding site and the polo-box domain in PLK1 present crucial interaction sites for these inhibitors, aiming to disrupt the protein's function. However, designing potent and selective small-molecule inhibitors can be challenging, requiring a deep understanding of protein-ligand interaction mechanisms at these binding sites. In this context, our study leverages the fragment molecular orbital (FMO) method to explore these site-specific interactions in-depth. Through the FMO approach, we used the FMO method to elucidate the molecular mechanisms of small-molecule drug binding to these sites to design PLK1 inhibitors that are both potent and selective. Our investigation further entailed a comparative analysis of various PLK1 inhibitors, each characterized by distinct structural attributes. This comparison enhanced our understanding of the structure-activity relationships of these inhibitors, underscoring the efficacy of the FMO method in identifying critical binding features and predicting binding modes for small-molecule ligands. Furthermore, Our research spotlighted "hot spot" residues instrumental for selective and robust PLK1 binding. Our findings offer profound insights, priming the rational design of innovative potential PLK1 inhibitors with significant implications for developing anticancer therapeutics.

In this study, we investigate the structural changes, electronic properties, and charge redistribution within azo-bithiophene (Azo-BT) chemisorbed monolayers under different light stimuli using density functional theory and molecular dynamics simulations. We consider two types of switches, Azo-BT and BT-Azo, with different arrangements of the Azo and BT blocks counting from the anchor thiol group. The chemisorbed monolayers of pure cis- and trans-isomers with a surface concentration of approximately 2.7 molecules per nm2 are modeled on a gold surface using classical all-atom molecular dynamics. Our results reveal significant shrinkage of the BT-Azo layer under UV illumination, whereas the thicknesses of the Azo-BT layer remain comparable for both isomers. This difference in behavior is attributed to the ordering of the trans-molecules in the layers, which is more pronounced for Azo-BT, leading to a narrow distribution of the inclination angle to the gold surface. Conversely, both layers consisting of cis-switches exhibit disorder, resulting in similar brush heights. To study charge transfer within the immobilized layers, we analyze each snapshot of the layer and calculate mean charge transfer integrals using Nelsen’s algorithm for a number of interacting neighboring molecules. Combining these integrals with reorganization energies defined for the isolated molecules, we evaluate the charge transfer rates and mobilities for electron and hole hopping within the layers at room temperature based on Marcus’ theory. This research offers new perspectives for the innovative design of electrode surface modifications and provides insights into controlling charge transfer within immobilized layers using light triggers. Additionally, we identify molecular properties that are enhanced through specific molecular design, which contributes to the development of more efficient molecular switches for various electronic applications.

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the N-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.

Three-dimensional structure of six closely related hydrogenases from purple bacteria has been modeled by combining template-based and ab initio modeling approach. The results lead to conclusion that there should be 4Fe3S-cluster in the structure of these enzymes. Thus, these hydrogenases could drive attention for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of 4Fe3S-cluster's microenvironment showed intragroup heterogeneity. Possible function of the C-terminal part of the small subunit in membrane binding has been discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) has been carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in number of hydrophobic interactions and number of ionic interactions. Molecular tunnels were mapped in the models and compared with structures from PDB. Protein-protein docking showed that these enzymes could exchange electrons in oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E.coli, H. marinus, R. eutropha, S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvx. gelatinosus.

Prototype of a family of at least nine members, c-src tyrosine kinase is a therapeutically interesting target, because its inhibition might be of interest not only in a number of malignancies, but also in a diverse array of conditions, from neurodegenerative pathologies to certain viral infections. Computational methods in drug discovery are considerably cheaper than conventional methods and offer opportunities of screening very large numbers of compounds in conditions that would be simply impossible within the wet lab experimental settings. We have explored the use of global QSAR models and molecular ligand docking in the discovery of new c-src tyrosine kinase inhibitors. Using a data set of 1038 compounds from ChEMBL and 19 blocks of molecular descriptors, we have developed over 200 QSAR classification models, based on six machine learning algorithms and 17 feature selection methods. We have selected 49 with reasonably good performance (positive predictive value and balanced accuracy higher than 70% in nested cross validation) and the models were assembled by stacking with a simple majority vote and used for the virtual screening of over the “named” ZINC data set (over 100,000 compounds). 744 compounds were predicted by at least 50% of the QSAR models as active, 147 compounds were within the applicability domain and predicted by at least 75% of the models to be active. The latter 147 compounds were submitted to molecular ligand docking using Vina and Ledock, and a number of 90 were predicted to be active based on the binding energy. External data from CHEMBL and PUBCHEM confirmed that at least 7.83% (in the case of QSAR) or 6.67% (in the case of integrated QSAR and molecular docking) of the compounds are active on the c-src target.

With the increasing demand for energy worldwide, researchers from different fields have been striving to improve the sustainability and proper utilization of energy resources. Passive radiative cooling, as a natural energy transport method, can achieve cooling without additional external energy input. This review provides a comprehensive examination of passive radiative cooling, including its fundamental theories and latest development. A particular emphasis is placed on the diverse range of fields where passive radiative cooling has been applied, notably including but not limited to construction and architecture. The current state of applications, potential challenges that may arise with wider adaption and promising research directions for each field are thoroughly discussed. This review underscores the universal applicability and feasibility of passive radiative cooling and contributes to its future development by identifying promising areas for further exploration.

This study investigates the contribution of nano-alumina (nA: 1-3wt.% binder) to the performance of silica fume (SF-10%) blended mortar in ternary blended mortar. The fresh (workability, setting time) and hardened properties (compressive strength and thermal resistance (300 °C for 1 h)), were examined. Nano alumina (nA) contributed positively to the consistency of SF blended mortar such that similar workability could be achieved with OPC when 3% nA was added. The initial and final setting time of 180 and 220 mins were recorded in SF blended mortar and reduced by 18.4 and 21.8%, respectively by adding 3%nA. The optimum mixture that contained 10%SF and 2%nA had 3-d and 28-d compressive strengths of 28 and 43.2 MPa. In the absence of nA, this reduced by 14.3% and 29.4% while it reduced by 25.2% and 16.7%, respectively in OPC mortar. The main products characterizing SF-nA ternary blended binder with dense microstructural density were nepheline and tobermorite. Besides, it is more susceptible to carbonation despite its superior performance in thermal resistance when compared to SF blended and OPC mortars.

This paper describes the packaging models that are fundamental for the design of ultra-high-performance concrete (UHPC), and their evolution. They are divided into two large groups: continuous and discrete models. The latter are those that provide the best answer in obtaining an adequate simulation of the packing of the particles up to nanometric size. This includes the interaction among the particles by means of loosening and wall coefficients, allowing a simulation of the virtual and real compactness of such particles. In addition, a relationship between virtual and real compactness is obtained, through the compaction index, which may simulate the energy of compaction that the particles undergo in their placement in the mold. The use of last-generation additives allows such models to be implemented with water-cement (w/c) ratios close to 0.18. However, the premise of maximum packing as a basic pillar for the production of UHPC should not be the only one. The cement hydration process affected by nanoadditions and the ensuing effectiveness in the properties in both fresh and hardened state according to the respective percentages in the mixture should also be studied. An adequate ratio and proportion of these additions may lead to an obtaining of better results even with lower levels of compactness.

At present, the world is now passing a very far different time than normal situation due to the COVID-19 pandemic crisis. The global life-style and human civilization is currently progressing with down-stream that affecting almost every sectors necessary for human civilizations except the current environmental situation. To control the COVID-19 spreading, most of the countries are following lockdown process that reduces human mobility, thus reducing the CO2 emission to the environment. Though the COVID-19 pandemic is a blessing for the present environment, however, the post-COVID world will face a massive thrust of energy and only conventional energy resources may not be enough to mitigate the energy demands. Solar power generation technology mainly the photovoltaic (PV) systems and their advancement can be the leading possibilities to minimize the gap between the power demand and generation. It is now time to think how we can improve the PV power generation in future and the post-COVID world. In this encyclopaedia communication, we report on Nano-technological approach to improve the conversion efficiency of GaAs solar cells. We have designed and optimized several types of nano-structured assemblies that can be implemented to reduce the front surface incident light reflection losses thus can assist to improve the conversion efficiency of GaAs solar cells.

The science on the anthropogenic airborne aerosols impacting upon the World Heritage marble monument, the Taj Mahal, at Agra has been studied in the light of modern physico-chemical approaches. The study is an effort to understand yet unrecognized airborne species which were found on the surface of the Taj Mahal monument. These species have been analyzed in the light of current analytical methods to impart characterization features and their possible impacts on the surface of the marble. Chemical constituents of these substrates which were incorporated over the top surface of the monument have been identified. Interestingly, the carbon particulates which were thought in the micro level, popularly called “particulate matters” has now been identified even in the nano domain entity, which are chemically more reactive, have been found on the surface of the monument. Because of their high chemical activity these nano carbons do play newer chemistry in the presence of air and sunlight generating several reactive oxygen species (ROS).These ROS are capable to respond to complicated chemical reactions on the surface of the marble in association with deposited cyanophyceae and other deposits of plant origin causing rapid degradation. This study provides the nature of onslaught borne out by such monument exposed under the prevalent smoggy environmental scenario.

The effect of γ-ray irradiation on surface plasmon resonance (SPR) sensing capability of refractive index (n = 1.418–1.448) of the silica glass optical fiber comprised of germano-silicate glass cladding embedded with Au nano-particles (NPs) was investigated. As the γ-ray irradiation increased from 1 hour to 3 hours with the dose rate of 1,190 Gy/h, the morphology of the Au NPs and the SPR spectrum were found to change. The average diameter of Au NPs increased with the aspect ratio from 1 to 2 and the nano-particles became grown to the clusters. The SPR peak wavelength shifted towards longer wavelength with the increase of total dose of γ-ray irradiation regardless of the corresponding refractive indices. The SPR sensitivities (wavelength/refractive index unit, nm/RIU) also increased from 407 nm/RIU to 3,553 nm/RIU, 1,483 nm/RIU, and 2,335 nm/RIU after the γ-ray irradiation at the total dose of 1,190 Gy, 2,380 Gy, and 3,570 Gy, respectively.

Biocompatible polymeric materials with potential to form functional structures in association with different therapeutic molecules have a high potential for biological, medical and pharmaceutical applications. Therefore, the protective capability of the inclusion nano-Complex formed between the sodium salt of poly(maleic acid-alt-octadecene) and a β-lactam drug (ampicillin trihydrate) on the chemical, enzymatic and biological degradation was evaluated. PAM-18Na was produced and characterized as reported previously. The formation of polymeric hydrophobic aggregates in aqueous solution was determined, using pyrene as a fluorescent probe. Furthermore, the formation of polymer-drug nano-complexes was characterized by Differential Scanning Calorimetry-DSC, viscometric, ultrafiltration/centrifugation assays, zeta potential and size measurements by dynamic light scattering-DLS. The PAM-18Na capacity to avoid the chemical degradation was studied through stress stability tests. The enzymatic degradation was evaluated from a pure β-lactamase, while the biological degradation was determined by different β-lactamase producing Staphylococcus aureus strains. When ampicillin was associated with PAM-18Na, the half-life time in acidic conditions increased, whereas both the enzymatic degradation and the minimum inhibitory concentration decreased to a 90 and 75%, respectively. These results suggest a promissory capability of this polymer to protect the β-lactam drugs against chemical, enzymatic and biological degradation.

Precise classification of sarcomas is crucial to drive optimal clinical management. In this prospective, multicenter, observational study within the Hellenic Group of Sarcoma and Rare Cancers (HGSRC) we assessed the effect of expert pathology review, coupled with the application of molecular diagnostics, on diagnosis and management of sarcoma patients. Newly diagnosed sarcoma patients were addressed by their physicians to one of the two sarcoma pathologists of HGSRC for histopathological diagnostic assessment. RNA next-generation sequencing was per-formed to all samples, using a platform targeting 86 sarcoma gene fusions. Additional molecular methods were performed on the opinion of the expert pathologist. Therefore, the expert pathologist provided a final diagnosis based on the histopathological findings and, when necessary on molecular tests. In total, 128 specimens from 122 patients were assessed. Among the 119 cases in which there was a preliminary diagnosis by a non-sarcoma pathologist, there were 37 modifications in diagnosis (31.1%) by the sarcoma pathologist, resulting in 17 (14.2%) modifications in management. Among the 110 cases in which molecular tests were performed, there were 29 modifications in diagnosis (26.4%) through the genomic results, resulting in 12 (10.9%) modifications in management. Our study confirms that expert pathology review is of utmost importance for the optimal sarcoma diagnosis and management and should be assisted by molecular methods in selected cases.

Exploring therapeutic options is crucial in the ongoing COVID-19 pandemic caused by SARS-CoV-2. Nirmatrelvir, a potent inhibitor targeting the SARS-CoV-2 Mpro, shows promise as an antiviral treatment. Additionally, Ivermectin, a broad-spectrum antiparasitic drug, has demonstrated effectiveness against the virus in laboratory settings. However, its clinical implications are still debated. Using computational methods such as molecular docking and 100 ns molecular dynamics simulations, we investigated how Nirmatrelvir and Ivermectin interact with SARS-CoV-2 Mpro(A). Calculations using density functional theory have been instrumental in elucidating the behavior of isolated molecules, primarily by analyzing the frontier molecular orbitals. Our analysis revealed distinct binding patterns: Nirmatrelvir formed strong interactions with amino acids like MET49, MET165, HIS41, HIS163, HIS164, PHE140, CYS145, GLU166, and ASN142, showing stable binding with a root mean square deviation (RMSD) of around 2.0 Å. On the other hand, Ivermectin interacted with THR237, THR239, LEU271, LEU272, and LEU287, displaying an RMSD of 1.87 Å, indicating enduring interactions. Both ligands stabilized Mpro(A), with Ivermectin showing stability and persistent interactions despite forming fewer hydrogen bonds. These findings offer detailed insights into how Nirmatrelvir and Ivermectin bind to the SARS-CoV-2 main protease, providing valuable information for potential therapeutic strategies against COVID-19.

The novel coronavirus disease (COVID-19) pandemic has resulted in over 720 million confirmed cases and 7 million deaths worldwide, with insufficient treatment options. Innumerable efforts are being made around the world for faster identification of therapeutic agents to treat the deadly disease. Postacute sequelae of SARS-CoV-2 infection or COVID-19 (PASC), also called Long COVID, is still being understood and lacks treatment options as well. A growing list of drugs are being suggested by various in silico, in vitro and ex vivo models, however currently only two treatment options are widely used: the RNA-dependent RNA polymerase (RdRp) inhibitor remdesivir, and the main protease inhibitor nirmatrelvir in combination with ritonavir. Computational drug development tools and in silico studies involving molecular docking, molecular dynamics, entropy calculations and pharmacokinetics can be useful to identify new targets to treat COVID-19 and PASC, as shown in this work and our recent paper that identified alendronate as a promising candidate. We have now investigated all bisphosphonates which can bind competitively to nidovirus RdRp-associated nucleotidyl (NiRAN) transferase domain, and systematically down selected seven candidates (CHEMBL608526, CHEMBL196676, CHEMBL164344, CHEMBL4291724, CHEMBL4569308, CHEMBL387132, CHEMBL98211), two of which closely resemble the approved drugs minodronate and zoledronate. This work and our recent paper together provide an in silico mechanistic explanation for alendronate and zoledronate users having dramatically reduced odds of SARS-CoV-2 testing, COVID-19 diagnosis, and COVID-19-related hospitalizations, and indicate that similar observational studies with minodronate could be valuable.

Dysregulation of the arsenal of cells, growth factors, cytokines, proteases, and proteins involved in wound healing (WH), could delay the healing process. Plants and plant-derived molecules (PDMs) have been used as medicines for skin wounds. This study aimed to select and evaluate the pro-healing capacity of PMDs. Thirty-three PDMs and 10 therapeutic targets (TTs) were chosen for molecular docking and PDMs: aristolochic acid (AA), α-copaene, selinenes, β-caryophyllene (BC), and BCoxide, and TTs: metalloproteinase (MMP) 3, MMP13, and tumor necrosis factor (TNF α) for molecular dynamics. The bests inhibitor was AA, but because of its toxicity, BC and BCoxide were chosen for evaluation in HaCat cells and BALB/c mice excisional model. Both compounds were not toxic, and higher percentages of lesion area closure (LAC) were induced by BC treatment (p<0.05). All mice healed; however, an initial delay of LAC was induced by 0.05, 0.1% BCoxide, 0.1% BC, and allantoin. At the end of treatment, lower numbers of mast cells, level of cellular infiltrates (except 1% BCoxide and 0.05, 0.5%BC), epidermal thickness tendency (except 0.1, 0.5% BCoxide), and higher values of SC-thickness, and collagen fibers only by 0.5% BC treatment compared with untreated control (p<0.05) were observed. Our results show that BC is a promising multitarget candidate for wound healing treatment and optimization campaigns.

Most existing cancer therapies negatively affect normal tissue as well as cancerous tissue. A potentially effective strategy for treating cancer that precludes off-target damage and could be an option for most patients would involve targeting one or more mutations that are ubiquitous in the given patient’s tumor(s). To effect this strategy, one would employ multi-region sequencing of a patient’s primary tumor and metastases to seek out mutations that are shared between all or at least most regions. Once the target or targets are known, one would ideally rapidly generate a molecular switch for at least one of said ubiquitous mutations that can distinguish the mutated DNA, RNA, or protein from the wild-type version and subsequently trigger a therapeutic response. I propose that the therapeutic response involve the replication of an oncolytic virus or intracellular bacterium, as any mutation can theoretically be detected by a vector that enters the cell - and automatic propagation could be very helpful. Moreover, the mutation “signal” can be easily enhanced through transcriptional and translational (if the target is an intracellular protein) enhancement. Importantly, RNA may make the best target for the molecular switches in terms of amplification of the signal and ease of targeting.

Thrombosis has threatened human health in past decades. Bacillus nattokinase is a potential thrombolytic drug without side-effect and low cost and has been introduced into the consumer market as a functional food or dietary supplement. This review firstly summarizes the biodiversity sources and fermentation process of nattokinase, and systematically expounds the structure, cata-lytic mechanism and enzymatic properties of nattokinase; In view of the problems of low fermen-tation yield, insufficient activity and stability of nattokinase, this review discusses the heterologous expression of nattokinase in different microbial hosts, and summarizes the protein and genetic en-gineering progress of nattokinase-producing strains; Finally, this review summarizes the clinical application of nattokinase.

The past two decades have witnessed the introduction of and then a steady increase in the use of computational techniques in the study and development of molecularly imprinted polymers (MIPs). Molecular dynamics (MD) based studies have had a significant role in this development as they can provide insights concerning the mechanisms governing the molecular level events underlying MIP synthesis and MIP-ligand interactions and can be used for the identification of preferred monomer compositions and for the prediction of MIP properties. We here review the role that MD has played in the development of molecular imprinting and examine the different types of MD strategies that have been used, including their advantages and challenges. Recent trends in the application of MD to the study of MIPs are presented, along with a perspective on the future importance of MD-based studies for the development of molecular imprinting science and technology.

This research aims to find out whether the synthetic 1, 2, 4-triazine and its derivatives have antifungal effects and can protect humans from infection with Candida albicans. Molecular docking and molecular dynamic simulation are widely used in modern drug design to target a We are interested in using molecular docking and molecular dynamics modelling to investigate the interaction between the derivatives of 1, 2, 4-triazine and the resulting lanosterol 14 - demethylase (CYP51) of Candida albicans The inhibition of Candida albicans CYP51 is the main goal of our research. The 1, 2, 4-triazine and its derivatives have been docked to the CYP51 enzyme, which is involved in Candida albicans Multidrug Drug Resistance (MDR). Autodock tools were used to identifying the binding affinities of molecules against the target proteins. Compared to conventional fluconazole, the molecular docking results indicated that each drug has a high binding affinity for CYP51 proteins and forms unbound interactions and hydrogen bonds with their active residues and surrounding allosteric residues. The docking contacts were made using a 10 ns MD simulation with nine molecules. RMSD, RMSF, hydrogen bonds, and the Rg all confirm these conclusions. In addition, these compounds were expected to have a favorable pharmacological profile and low toxicity. The compounds are being offered as scaffolds for the development of new antifungal drugs and as candidates for future in vitro testing.

Mutations affecting codon 172 of the isocitrate dehydrogenase 2 (IDH2) gene define a subgroup of sinonasal undifferentiated carcinomas (SNUCs) with a relatively favorable prognosis and a globally hypermethylated phenotype. They are also recurrent (along with IDH1 mutations) in gliomas, acute myeloid leukemia, and intrahepatic cholangiocarcinoma. Commonly reported mutations, all associated with aberrant IDH2 enzymatic activity, include R172S, R172T, R172G, and R172M. We present a case of SNUC with a never-before-described IDH2 mutation, R172A. Our report compares the methylation pattern of our sample to other cases from the GEO database. Hierarchical clustering suggests a strong association between our sample and other IDH-mutant SNUCs and a clear distinction between sino-nasal normal tissues and tumors. Principal component analysis (PCA), using 100 principal components explaining 94.5% of the variance, shows the position of our sample within 1.02 standard deviation of the other IDH-mutant SNUCs. Molecular modeling analysis of the IDH2 R172A versus other R172 variants provides a structural explanation to how they affect the protein active site. Our findings thus suggest that the R172A mutation in IDH2 confers a gain of function similar to other R172 mutations in IDH2, resulting in a similar hypermethylated profile.

Auxins are chemical compounds of wide interest, mostly due to their role in plant metabolism and development. Since the latter half of the XX century, synthetic auxins have been used as herbicides, presenting notable advantages, such as low toxicity in humans. As of today, extensive descriptions of syntetic and natural auxins have been made; yet studies centered on the molecular recognition process of auxins are scarce. Herein, we present a comprehensive in silico characterization of auxin receptor TIR1, using structure based methods to aid de novo design of putative ligands. In addition, we conducted binding site characterization using cosolvent molecular dynamics and enhanced sampling simulations with reference ligands. We also present a database of putative auxins and decoy compounds which can aid further studies focusing on synthetic auxin design. To the best of our knowledge, this study is the first of its kind focusing on TIR1.

Abstract: The Willows, belonging to the genus Salix, encompass a vast array of species and hybrids, totaling between 330 to 500 species along with approximately 200 hybrids. These plants are found across continents such as Africa, North America, Europe, and Asia, exhibiting diverse forms ranging from trees to shrubs and prostrate plants. Traditionally, Willows have been utilized in folk medicine due to their rich reservoir of biologically active compounds, with salicin being a notable example, serving as a prodrug for salicylic acid.The chemical composition of Willows is highly diverse, with 322 secondary metabolites identified thus far. These include various classes such as flavonoids (94 types encompassing flavonols, flavones, flavanones, isoflavones, flavan-3-ols like catechins and procyanidins, chalcones, dihydrochalcone, anthocyanins, and dihydroflavonols), phenolic glycosides (76), organic acids (28), non-phenolic glycosides (17), sterols, and terpenes (17), simple phenolics (13), lignans (7), as well as volatiles and fatty acids (69). This rich chemical di-versity underpins the various pharmacological activities exhibited by Willows. The pharmacological properties attributed to Willows are extensive and include analgesic, an-ti-inflammatory, antioxidant, anticancer, cytotoxic, antidiabetic, antimicrobial, antiobesity, neuroprotective, and hepatoprotective effects. These properties make Willows a subject of con-siderable interest in the fields of medicine and pharmacology. In summary, Willows represent a valuable natural resource with a diverse chemical composition and a wide range of pharmacological activities. This study aimed to enhance our comprehension of the medicinal characteristics of willow bark extract, focusing on its antimicrobial properties. This investigation holds significance in validating the traditional usage of willow bark and investi-gating its potential utility in contemporary medicine.

Calicioids form a research field that has encompassed ascomycetous fungi with stalked ascomata similar to those of the lichen genus Calicium. Early generic circumscriptions in calicioid lichens and fungi were mainly based on morphological and secondary chemistry information. After the introduction of molecular data, taxonomy in the group has been reconsidered. Here, based on a broad geographical sampling, Coniocybe Ach. was revised using molecular and morphological features. Three loci (ITS, LSU and rpb1) were compared to infer its phylogenetic position, and a total of 52 new sequences (14 ITS, 24 LSU and 14 rpb1) were produced. Coniocybe was revised and emended to include, apart for its type C. furfuracea, also C. brachypoda and C. confusa. In addition, a new species Coniocybe eufuracea, was described, and a key to the species of Coniocybe provided.

Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its recent prominence in Bio-medical Engineering for biopolymer materials has recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: A) Computer-aided design (CAD/CAM), B) Finite Element Analysis, and C) Molecular Dynamic Simulations. This review centers on Molecular Dynamics (MD) simulations in biopolymers, analyzing structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, generating spatial trajectories for each atom, providing insights into properties like water absorption on biopolymer surfaces and interactions with solid surfaces, crucial for biomaterial assessment. This review offers readers a comprehensive overview of the diverse applications of Molecular Dynamics (MD) simulations on biopolymers. Furthermore, it emphasizes the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.

Diffuse intrinsic pontine glioma (DIPG), affecting children aged 4-7 years, is a rare, aggressive tumor that originates in the pons and then spreads to nearby tissue. DIPG is the leading cause of death for pediatric brain tumors due to its infiltrative nature and inoperability. Radiotherapy has only a palliative effect in stabilizing symptoms. In silico and preclinical studies identified ONC201, as a cytotoxic agent against some human cancer cell lines, including DIPG ones. Single crystal X-ray analysis of the complex of the human mitochondrial caseinolytic serine protease type C (hClpP) and ONC201 (PDB ID: 6DL7) allowed to identify hClpP as its main target. Hyperactivation of hClpP causes damage to mitochondrial oxidative phosphorylation and cell death. In some DIPG patients, receiving ONC201, an acquired resistance was observed. In this context, a wide program was initiated to discover original scaffolds for new hClpP activators to treat ONC201-non-responding patients. Harmaline, a small molecule belonging to the chemical class of β -carboline, was identified through Fingerprints for Ligands and Proteins (FLAP), a structure-based Virtual Screening approach. Molecular dynamics simulations and a deep in vitro investigation showed interesting information on the interaction and activation of hClpP by harmaline.