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Abstract Background Identifying therapeutic inhibitors of crucial enzymes involved in the peptidoglycan biosynthesis pathway is pivotal for developing new treatments against multidrug-resistant Enterococcus faecalis V583. MurM, an essential enzyme in this pathway, plays a significant role in the bacterium’s cell wall synthesis, making it an attractive druggable target for novel antimicrobial strategies. This study explored the potential of natural compounds as inhibitors of MurM, aiming to discover promising drug candidates that could serve as the foundation for future therapeutic development. Methods The three-dimensional structure of MurM was predicted, optimized, and its binding pocket was analyzed by comparing it with related structures. Over 4,70,000 natural compounds from the COCONUT database were subjected to virtual high-throughput screening (vHTS). The top lead candidates were selected based on their Lipinski’s profile, ADME profile, toxicity profile, estimated binding free energy (ΔG) and estimated inhibition constant (Ki). Interaction pattern analysis was used to evaluate the non-covalent interactions between the inhibitors and key residues in MurM’s binding pocket. Molecular dynamics simulations were performed over 300 ns to assess the structural stability and impact of these inhibitors on MurM’s enzyme. Results Three lead compounds—CNP0056520, CNP0126952, and CNP0248480—were identified and prioritized with estimated ΔG ranging from − 9.35 to -7.9 kcal/mol. Molecular dynamics simulations revealed minimal impact on MurM’s overall structure and dynamics, with the candidate inhibitors forming stable protein-ligand complexes. These interactions were supported by several non-covalent interactions between the candidate inhibitors and key residues within MurM’s binding pocket. Conclusion These findings suggest that the identified natural product candidates could serve as promising inhibitors of MurM, potentially leading to novel therapeutics targeting cell wall biosynthesis in multidrug-resistant E. faecalis.

Abstract An abnormal growth or fatty mass of cells in the brain is called a tumor. They can be either healthy (normal) or become cancerous, depending on the structure of their cells. This can result in increased pressure within the cranium, potentially causing damage to the brain or even death. As a result, diagnostic procedures such as computed tomography, magnetic resonance imaging, and positron emission tomography, as well as blood and urine tests, are used to identify brain tumors. However, these methods can be labor-intensive and sometimes yield inaccurate results. Instead of these time-consuming methods, deep learning models are employed because they are less time-consuming, require less expensive equipment, produce more accurate results, and are easy to set up. In this study, we propose a method based on transfer learning, utilizing the pre-trained VGG-19 model. This approach has been enhanced by applying a customized convolutional neural network framework and combining it with pre-processing methods, including normalization and data augmentation. For training and testing, our proposed model used 80% and 20% of the images from the dataset, respectively. Our proposed method achieved remarkable success, with an accuracy rate of 99.43%, a sensitivity of 98.73%, and a specificity of 97.21%. The dataset, sourced from Kaggle for training purposes, consists of 407 images, including 257 depicting brain tumors and 150 without tumors. These models could be utilized to develop clinically useful solutions for identifying brain tumors in CT images based on these outcomes.

Acinetobacter baumannii is one of the emerging causes of hospital acquired infections and this bacterium, due to multi-drug resistant and Extensive Drug resistant has been able to develop resistance against the antimicrobial agents that are being used to eliminate it. A.baumannii has been the cause of death in immune compromised patients in hospitals. Hence it is the urgent need of time to find potential inhibitors for this bacterium to cease its virulence and affect its survival inside host organisms. The Dihydrofolate reductase enzyme, which is an important biocatalyst in the conversion of Dihydrofolate to Tetrahydrofolate, is an important drug target protein. In the present study high throughput screening is used to identify the inhibitors of this enzyme. The prioritized ligand molecular candidates identified through virtual screening for the substrate binding site of the predicted model are Z1447621107, Z2604448220 and Z1830442365. The Molecular Dynamics Simulation study suggests that potential inhibitor of the Dihydrofolate reductase enzyme would prevent bacteria from completing its life cycle, affecting its survival. Finally the complexes were analysed for binding free energy of the Dihydrofolate reductase enzyme complexes with the ligands.

Digitoxin is a cardiac glycoside used to treat heart failure and heart arrhythmia. However, its therapeutic concentration range is very narrow. High doses of digitoxin are associated with severe side effects; therefore, it is necessary to develop the delivery system which can control the plasma levels of it. In this context, the binding of lysozyme, an important protein having many applications, with digitoxin has been studied to see the ability of the former as a carrier. The studies were carried out using both experimental and computational methods. The intrinsic fluorescence of lysozyme increased on the addition of digitoxin. Fluorescence results suggested that there was a strong interaction between lysozyme and digitoxin which was favored, mainly, by hydrophobic forces. Further, digitoxin affected the secondary structure of lysozyme slightly by causing the partial unfolding of lysozyme. The preferred binding site of digitoxin within lysozyme was the large cavity of the protein. Molecular docking studies also established the principal role of hydrophobic forces in the binding with a significant support of hydrogen bonding. Frontier molecular orbitals of free digitoxin and in complexation with lysozyme were also computed and discussed. The findings from molecular dynamics simulation studies elucidate that, when contrasted with the first and third conformations of the digitoxin-bound lysozyme complex, the second conformation promotes structural stability, reduces flexibility, and enhances the compactness and folding properties of lysozyme. The overall study shows that lysozyme could act as a potential carrier for digitoxin in pharmaceutical formulations.

The need for a vaccine/inhibitor design has become inevitable concerning the emerging epidemic and pandemic viral infections, and the recent outbreak of the influenza A (H1N1) virus is one such example. From 2009 to 2018, India faced severe fatalities due to the outbreak of the influenza A (H1N1) virus. In this study, the potential features of reported Indian H1N1 strains are analyzed in comparison with their evolutionarily closest pandemic strain, A/California/04/2009. The focus is laid on one of its surface proteins, hemagglutinin (HA), which imparts a significant role in attacking the host cell surface and its entry. The extensive analysis performed, in comparison with the A/California/04/2009 strain, revealed significant point mutations in all Indian strains reported from 2009 to 2018. Due to these mutations, all Indian strains disclosed altered features at the sequence and structural levels, which are further presumed to be associated with their functional diversity as well. The mutations observed with the 2018 HA sequence such as S91R, S181T, S200P, I312V, K319T, I419M, and E523D might improve the fitness of the virus in a new host and environment. The higher fitness and decreased sequence similarity of mutated strains may compromise therapeutic efficacy. In particular, the mutations observed commonly, such as serine-to-threonine, alanine-to-threonine, and lysine-to-glutamine at various regions, alter the physico-chemical features of receptor-binding domains, N-glycosylation, and epitope-binding sites when compared with the reference strain. Such mutations render diversity among all Indian strains, and the structural and functional characterization of these strains becomes inevitable. In this study, we observed that mutational drift results in the alteration of the receptor-binding domain, the generation of new variant N-glycosylation along with novel epitope-binding sites, and modifications at the structural level. Eventually, the pressing need to develop potentially distinct next-generation therapeutic inhibitors against the HA strains of the Indian influenza A (H1N1) virus is also highlighted here.

The coexistence of ceftazidime, which is a popular third-generation of cephalosporin antibiotic, with ubiquitous paracetamol or acetaminophen, is very likely because the latter is given to the patients to reduce fever due to bacterial infection along with an antibiotic such as the former. Therefore, in this study, we investigated the detailed binding of ceftazidime with plasma protein, human serum albumin (HSA), in the absence and presence of paracetamol using spectroscopic techniques such as fluorescence, UV-visible, and circular dichroism, along with in silico methods such as molecular docking, molecular dynamics simulations, and MM/PBSA-based binding free energy analysis. The basic idea of the interaction was attained by using UV-visible spectroscopy. Further, fluorescence spectroscopy revealed that there was a fair interaction between ceftazidime and HSA, and the mechanism of the quenching was a dynamic one, i.e., the quenching constant increased with increasing temperature. The interaction was, primarily, reinforced by hydrophobic forces, which resulted in the partial unfolding of the protein. Low concentrations of paracetamol were ineffective in affecting the binding of ceftazidime with has; although, a decrease in the quenching and binding constants was observed in the presence of high concentrations of the former. Competitive binding site experiments using warfarin and ibuprofen as site markers revealed that ceftazidime neither binds at drug site 1 or at drug site 2, articulating another binding site, which was confirmed by molecular docking simulations.

A. baumannii is a ubiquitously found gram-negative, multi-drug resistant bacterial species from the ESKAPE family of pathogens known to be the causative agent for hospital-acquired infections such as pneumonia, meningitis, endocarditis, septicaemia and urinary tract infections. A. baumannii is implicated as a contributor to bloodstream infections in approximately 2% of all worldwide infections. Hence, exploring novel therapeutic agents against the bacterium is essential. LpxA or UDP-N-acetylglucosamine acetyltransferase is an essential enzyme important in Lipid A biosynthesis which catalyses the reversible transfer of an acetyl group on the glucosamine 3-OH of the UDP-GlcNAc which is a crucial step in the biosynthesis of the protective Lipopolysaccharides (LPS) layer of the bacteria which upon disruption can lead to the elimination of the bacterium which delineates LpxA as an appreciable drug target from A. baumannii. The present study performs high throughput virtual screening of LpxA against the enamine-HTSC-large-molecule library and performs toxicity and ADME screening to identify the three promising lead molecules subjected to molecular dynamics simulations. Global and essential dynamics analysis of LpxA and its complexes along with FEL and MM/PBSA based binding free energy delineate Z367461724 and Z219244584 as potential inhibitors against LpxA from A. baumannii.

Microfluidic systems have received increased attention due to their wide variety of applications, from chemical sensing to biological detection to medical analysis. Microfluidics used to be fabricated by using etching techniques that required cleanroom and aggressive chemicals. However, another microfluidic fabrication technique, namely, soft lithography, is less expensive and safer compared to former techniques. Polydimethylsiloxane (PDMS) has been widely employed as a fabrication material in microfluidics by using soft lithography as it is transparent, soft, bio-compatible, and inexpensive. In this study, a 3D multi-layer PDMS suspended microfluidics fabrication process using soft lithography is presented, along with its manufacturing issues that may deteriorate or compromise the microsystem’s test results. The main issues considered here are bonding strength and trapped air-bubbles, specifically in multi-layer PDMS microfluidics. In this paper, these two issues have been considered and resolved by optimizing curing temperature and air-vent channel integration to a microfluidic platform. Finally, the suspended microfluidic system has been tested in various experiments to prove its sensitivity to different fluids and flow rates.

With the advancement of nanotechnology, the nano-bio-interaction field has emerged. It is essential to enhance our understanding of nano-bio-interaction in different aspects to design nanomedicines and improve their efficacy for therapeutic and diagnostic applications. Many researchers have extensively studied the toxicological responses of cancer cells to nano-bio-interaction, while their mechanobiological responses have been less investigated. The mechanobiological properties of cells such as elasticity and adhesion play vital roles in cellular functions and cancer progression. Many studies have noticed the impacts of cellular uptake on the structural organization of cells and, in return, the mechanobiology of human cells. Mechanobiological changes induced by the interactions of nanomaterials and cells could alter cellular functions and influence cancer progression. Hence, in addition to biological responses, the possible mechanobiological responses of treated cells should be monitored as a standard methodology to evaluate the efficiency of nanomedicines. Studying the cancer-nano-interaction in the context of cell mechanics takes our knowledge one step closer to designing safe and intelligent nanomedicines. In this review, we briefly discuss how the characteristic properties of nanoparticles influence cellular uptake. Then, we provide insight into the mechanobiological responses that may occur during the nano-bio-interactions, and finally, the important measurement techniques for the mechanobiological characterizations of cells are summarized and compared. Understanding the unknown mechanobiological responses to nano-bio-interaction will help with developing the application of nanoparticles to modulate cell mechanics for controlling cancer progression.

Bone exhibits piezoelectric properties. Thus, electrical stimulations such as pulsed electromagnetic fields (PEMFs) and stimuli-responsive piezoelectric properties of scaffolds have been investigated separately to evaluate their efficacy in supporting osteogenesis. However, current understanding of cells responding under the combined influence of PEMF and piezoelectric properties in scaffolds is still lacking. Therefore, in this study, we fabricated piezoelectric scaffolds by functionalization of polycaprolactone-tricalcium phosphate (PCL-TCP) films with a polyvinylidene fluoride (PVDF) coating that is self-polarized by a modified breath-figure technique. The osteoinductive properties of these PVDF-coated PCL-TCP films on MC3T3-E1 cells were studied under the stimulation of PEMF. Piezoelectric and ferroelectric characterization demonstrated that scaffolds with piezoelectric coefficient d33 = −1.2 pC/N were obtained at a powder dissolution temperature of 100 °C and coating relative humidity (RH) of 56%. DNA quantification showed that cell proliferation was significantly enhanced by PEMF as low as 0.6 mT and 50 Hz. Hydroxyapatite staining showed that cell mineralization was significantly enhanced by incorporation of PVDF coating. Gene expression study showed that the combination of PEMF and PVDF coating promoted late osteogenic gene expression marker most significantly. Collectively, our results suggest that the synergistic effects of PEMF and piezoelectric scaffolds on osteogenesis provide a promising alternative strategy for electrically augmented osteoinduction. The piezoelectric response of PVDF by PEMF, which could provide mechanical strain, is particularly interesting as it could deliver local mechanical stimulation to osteogenic cells using PEMF.

Understanding how cells sense mechanical forces, and how respond biologically to themis an interesting and quickly-progressing area. Cells within their microenvironment are subjected tovarious physical forces such as mechanical loads and shear stress. Cells respond and adjust to theseforces by mechanotransduction mechanism in which deformation and mechanical forces are convertedinto biomechanical signals. To quantify mechanotransduction responses and to correctly interpretthe behavior of cell under in vitro stimulation, magnitude and distribution of the stresses on the cellmembrane should be characterized. In this study, a 2D Finite Element Model is introduced to simulatethe deformation of individual benign (MCF10A) and malignant (MCF7) human breast cancer cellsunder hydrodynamic forces. A fluid-structure interaction method is implemented to model fluid flowand the adherent single cells inside a microchannel to study the nature of mechanical forces (viscousand pressure) and to determine their contribution to the deformation of cells. Due to the differentmechanical properties, cells respond differently to the forces exerted by the fluid flow. It was foundthat the maximum stress and strain take place at the interface of the adherent cell and channel wall. Also, under the same boundary conditions, nucleolus and cytoplasm of an individual malignant cellundergo more deformation comparing a single benign cell. Furthermore, it was observed that both two cell lines experience much more stress when their attached area to the substrate is reduced.

Colorectal cancer (CRC) is a fatal disease caused by the uncontrolled propagation and endurance of atypical colon cells. A person’s lifestyle and eating pattern have significant impacts on the CRC in a positive and/or negative way. Diet-derived phytochemicals modulate the microbiome as well as targeting colon cancer stem cells (CSCs) that are found to offer significant protective effects against CRC, which were organized in an appropriate spot on the paper. All information on dietary phytochemicals, gut microbiome, CSCs, and their influence on CRC were accessed from the various databases and electronic search engines. The effectiveness of CRC can be reduced using various dietary phytochemicals or modulating microbiome that reduces or inverses the progression of a tumor as well as CSCs, which could be a promising and efficient way to reduce the burden of CRC. Phytochemicals with modulation of gut microbiome continue to be auspicious investigations in CRC through noticeable anti-tumorigenic effects and goals to CSCs, which provides new openings for cancer inhibition and treatment.

In the present study optimization of the critical medium components for biosurfactant production by Bacillus subtilis using statistical experimental design was studied. Response surface methodology (RSM) was employed to determine the optimal level of the four medium variables (sucrose, yeast extract, FeSO47H2O and KH2PO4). Central composite design (CCD) of RSM was applied to study the four variables at five levels and biosurfactant concentration was measured as response. Regression coefficients were calculated by regression analysis and the model equation was determined. R2 value for biosurfactant (g/L) was calculated as 0.835 and it indicates that the model was well fitted with the experimental results. Surface plots were made and the maximum biosurfactant production (10 g/L) was predicted at the optimized values of sucrose 70 g/L, yeast extract 5 g/L, FeSO47H2O 0.055 g/L and KH2PO4 0.15 g/L. The obtained mathematical model was verified by performing the experiment with the predicted optimized values and the yield of bio-surfactant was found to be 9.78 g/L. Validation of the predicted model was fitted 97.8% with the experimental results conducted at the optimum conditions. Results of this statistical analysis showed that sucrose and yeast extract had found significant medium components for biosurfactant production.

Sea bass (Lateolabrax maculatus) is a kind of food material commonly consumed in daily life. In traditional Chinese medicinal books, it has been indicated that sea bass can be applied for managing many inflammation-associated conditions. However, the studies on the pharmacological mechanisms of inflammation of sea bass remain scarce. Hence, this study aims to investigate the molecular mechanisms of the anti-inflammatory activity of sea bass. Anti-inflammatory activities of sea bass were assessed using dextran sulfate sodium (DSS)-induced colitis in a mice model and lipopolysaccharide (LPS)-activated macrophages model. Low body weight and short colon length were observed in DSS-fed mice that were significantly recovered upon sea bass treatments. Moreover, the colon histopathology score showed that sea bass-treated mice had decreased crypt damage, focal inflammation infiltration and the extent of inflammation, suggesting that treatment with sea bass could attenuate intestinal inflammation. In addition, the in-vitro study conjointly indicated that sea bass could suppress the inflammatory mediators in LPS-activated macrophage by inhibiting the TLR4-linked pathway. The present findings demonstrated that sea bass has an inhibitory effect on TLR4 signaling; thus, it could be a promising candidate for treating inflammation-associated conditions. A further justification for the clinical application of sea bass in treating inflammation-associated conditions is necessary.

Bcl-2 protein is involved in cell apoptosis and is considered an interesting target for anti-cancer therapy. The present study aims to understand the stability and conformational changes of Bcl-2 upon interaction with the inhibitor venetoclax, and to explore other drug-target regions. We combined biophysical and in silico approaches to understand the mechanism of ligand binding to Bcl-2. Thermal shift assay (TSA) and urea electrophoresis showed a significant increase in protein stability upon venetoclax incubation, which is corroborated by molecular docking and molecular dynamics simulations. An 18 °C shift in Bcl-2 melting temperature was observed in the TSA, corresponding to a binding affinity multiple times higher than that of any other reported Bcl-2 inhibitor. This protein-ligand interaction does not implicate alternations in protein conformation, as suggested by SAXS. Additionally, bioinformatics approaches were used to identify deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) of Bcl-2 and their impact on venetoclax binding, suggesting that venetoclax interaction is generally favored against these deleterious nsSNPs. Apart from the BH3 binding groove of Bcl-2, the flexible loop domain (FLD) also plays an important role in regulating the apoptotic process. High-throughput virtual screening (HTVS) identified 5 putative FLD inhibitors from the Zinc database, showing nanomolar affinity toward the FLD of Bcl-2.

Measuring of fluid properties such as dynamic viscosity and density has tremendous potential for various applications from physical to biological to chemical sensing. However, it is almost impossible to affect only one of these properties, as dynamic viscosity and density are coupled. Hence, this paper proposes kinematic viscosity as a comprehensive parameter which can be used to study the effect of fluid properties applicable to various fluids from Newtonian fluids, such as water, to non-Newtonian fluids, such as blood. This paper also proposes an ideal microplatform, namely polymeric suspended microfluidics (SPMF3), with flow plane orthogonal to the bending plane of the structure, along with tested results of various fluids covering a wide range of engineering applications. Kinematic viscosity, also called momentum diffusivity, considers changes in both fluid intermolecular forces and molecular inertia that define dynamic viscosity and fluid density, respectively. In this study a 3D suspended polymeric microfluidic system (SPMF3) was employed to detect changes in fluid parameters such as dynamic viscosity and density during fluid processes. Using this innovative design along with theoretical and experimental results, it is shown that, in fluids, the variations of fluid density and dynamic viscosity are not easily comprehensible due to their interconnectivity. Since any change in a fluid will affect both density and dynamic viscosity, measuring both of them is necessary to identify the fluid or process status. Finally, changes in fluid properties were analyzed using simulation and experiments. The experimental results with salt-DI water solution and milk with different fat concentrations as a colloidal fluid show that kinematic viscosity is a comprehensive parameter that can identify the fluids in a unique way using the proposed microplatform.

Mushrooms have long been used for medicinal and food purposes for over a thousand years, but a complete elucidation of the health-promoting properties of mushrooms through regulating gut microbiota has not yet been fully exploited. Mushrooms comprise a vast, and yet largely untapped, source of powerful new pharmaceutical substances. Mushrooms have been used in health care for treating simple and common diseases, like skin diseases and pandemic diseases like AIDS. This review is aimed at accumulating the health-promoting benefits of edible mushrooms through gut microbiota. Mushrooms are proven to possess anti-allergic, anti-cholesterol, anti-tumor, and anti-cancer properties. Mushrooms are rich in carbohydrates, like chitin, hemicellulose, β and α-glucans, mannans, xylans, and galactans, which make them the right choice for prebiotics. Mushrooms act as a prebiotics to stimulate the growth of gut microbiota, conferring health benefits to the host. In the present review, we have summarized the beneficial activities of various mushrooms on gut microbiota via the inhibition of exogenous pathogens and, thus, improving the host health.