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BACKGROUND RESULTS CONCLUSION Mycotoxin contamination of food has been gaining increasing attention. Hidden mycotoxins that interact with biological macromolecules in food could make the detection of mycotoxins less accurate, potentially leading to the underestimation of the total exposure risk. Interactions of the mycotoxins alternariol (AOH) and alternariol monomethyl ether (AME) with high‐molecular glutenin were explored in this study.The recovery rates of AOH and AME (1, 2, and 10 μg kg−1) in three types of grains (rice, corn, and wheat) were relatively low. Molecular dynamics (MD) simulations indicated that AOH and AME bound to glutenin spontaneously. Hydrogen bonds and π‐π stacking were the primary interaction forces at the binding sites. Alternariol with one additional hydroxyl group exhibited stronger binding affinity to glutenin than AME when analyzing average local ionization energy. The average interaction energy between AOH and glutenin was −80.68 KJ mol−1, whereas that of AME was −67.11 KJ mol−1.This study revealed the mechanisms of the interactions between AOH (or AME) and high‐molecular glutenin using MD and molecular docking. This could be useful in the development of effective methods to detect pollution levels. These results could also play an important role in the evaluation of the toxicological properties of bound altertoxins. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Context: The interface of Hsp70-Bim protein–protein interaction (PPI) has been identified as a specific target for Chronic Myeloid Leukemia (CML) therapy and the specific inhibitors were developed to exhibit in vivo anti-leukemia activities. Herein, we explored the binding mechanism of a Hsp70-Bim inhibitor, 6-(cyclohexylthio)-3-((2-morpholinoethyl) amino)-1-oxo-1H-phenalene-2-carbonitrile (S1g-6), to Hsp70 at the atomic level by MD simulation. TYR-149, THR-222, ALA-223, and GLY-224 on Hsp70 were identified as four key residues that contribute to Hsp70/S1g-6 complex. Moreover, the site mutation validation demonstrated the TYR-149 of Hsp70 is a "hot-spot" in the Hsp70-Bim PPI interface. These results could benefit the design of further inhibitors to occupy the Bim binding site on the Hsp70 surface. Methods: The binding mechanism of S1g-6 and Hsp70 was predicted through the molecular dynamics (MD) method by Gromacs-2021.3. The MD simulation was performed with 100-ps NVT and 100-ps NPT ensemble, and the force field was chosen as the Charmm36 force field. The temperature was set as 300 K, the time step was 2 fs and the total MD simulation time was 500 ns. [ABSTRACT FROM AUTHOR]

Leishmaniasis is a public health concern, especially in Brazil and India. The drugs available for therapy are old, cause toxicity and have reports of resistance. Therefore, this paper aimed to carry out initial structure-activity relationships (applying molecular docking and dynamic simulations) of arylindole scaffolds against the pteridine reductase (PTR1), which is essential target for the survival of the parasite. Thus, we used a series of 43 arylindole derivatives as a privileged skeleton, which have been evaluated previously for different biological actions. Compound 7 stood out among its analogues presenting the best results of average number of interactions with binding site (2.00) and catalytic triad (1.00). Additionally, the same compound presented the best binding free energy (−32.33 kcal/mol) in dynamic simulations. Furthermore, with computational studies, it was possible to comprehend and discuss the influences of the substituent sizes, positions of substitutions in the aromatic ring and electronic influences. Therefore, this study can be a starting point for the structural improvements needed to obtain a good leishmanicidal drug. [ABSTRACT FROM AUTHOR]

In this work, we report a novel method for the label-free detection of cyanotoxin molecules based on a direct assay utilizing a graphene-modified surface plasmon resonance (SPR) aptasensor. Molecular dynamic simulation of the aptamer's interaction with cylindrospermopsin (CYN) reveals the strongest binding sites between C18–C26 pairs. To modify the SPR sensor, the wet transfer method of CVD monolayer graphene was used. For the first time, we report the use of graphene functionalized by an aptamer as a bioreceptor in conjunction with SPR for the detection of CYN. In a direct assay with an anti-CYN aptamer, we demonstrated a noticeable change in the optical signal in response to the concentrations far below the maximum tolerable level of 1 µg/L and high specificity. [ABSTRACT FROM AUTHOR]

In the present study, new structural variants of 4-hydroxyquinolinone-hydrazones were designed and synthesized. The structure elucidation of the synthetic derivatives 6a–o was carried out using different spectroscopic techniques including FTIR, 1H-NMR, 13C-NMR, and elemental analysis, and their α-glucosidase inhibitory activity was also determined. The synthetic molecules 6a–o exhibited good α-glucosidase inhibition with IC50 values ranging between 93.5 ± 0.6 to 575.6 ± 0.4 µM as compared to the standard acarbose (IC50 = 752.0 ± 2.0 µM). Structure–activity relationships of this series were established which is mainly based on the position and nature of the substituent on the benzylidene ring. A kinetic study of the active compounds 6l and 6m as the most potent derivatives were also carried out to confirm the mode of inhibition. The binding interactions of the most active compounds within the active site of the enzyme were determined by molecular docking and molecular dynamic simulations. [ABSTRACT FROM AUTHOR]

Plasmodium vivax (P. vivax) is one of the human's most common malaria parasites. P. vivax is exceedingly difficult to control and eliminate due to the existence of extravascular reservoirs and recurring infections from latent liver stages. Traditionally, licorice compounds have been widely investigated against viral and infectious diseases and exhibit some promising results to combat these diseases. In the present study, computational approaches are utilized to study the effect of licorice compounds against P. vivax Duffy binding protein (DBP) to inhibit the malarial invasion to human red blood cells (RBCs). The main focus is to block the DBP binding site to Duffy antigen receptor chemokines (DARC) of RBC to restrict the formation of the DBP–DARC complex. A molecular docking study was performed to analyze the interaction of licorice compounds with the DARC binding site of DBP. Furthermore, the triplicates of molecular dynamic simulation studies for 100 ns were carried out to study the stability of representative docked complexes. The leading compounds such as licochalcone A, echinatin, and licochalcone B manifest competitive results against DBP. The blockage of the active region of DBP resulting from these compounds was maintained throughout the triplicates of 100 ns molecular dynamic (MD) simulation, maintaining stable hydrogen bond formation with the active site residues of DBP. Therefore, the present study suggests that licorice compounds might be good candidates for novel agents against DBP-mediated RBC invasion of P. vivax. [ABSTRACT FROM AUTHOR]

One of the major challenges in type 2 diabetes is the inhibition of the enzyme alpha‐amylase, since many molecules targeting this enzyme based on or derived from medicinal plants have been synthesized to counteract the α‐amylase action. The present study investigated the in‐vitro and in‐silico antidiabetic capacities of three flavonol glucosides obtained from the plant Fumana montana Pomel using α‐amylase inhibition model. α‐amylase binding interaction with the studied compounds was examined using ultraviolet‐visible absorption spectroscopy technique. Molecular docking and ADMET prediction were also performed for the three phytoconstituents towards human pancreatic alpha‐amylase receptor. The in vitro results revealed that both compound FG1 and FG3 showed a higher antidiabetic activity (84.00±0.12 and 85.36±0.12 μg/ml respectively) than that of standard antidiabetic acarbose (91.12±0.11). The value of the binding free energy ranging from −31.66±0.07 to −32.68±0.03 KJ mol−1 demonstrated the spontaneity and the strong binding betweenα‐amylase and the studied phytoconstituents. Molecular docking study indicated the preferred binding site and binding mode, and further suggested that the binding mode of the three compounds to the target enzyme is of hydrogen bonding and hydrophobic forces. Further analysis by molecular dynamic simulation studies showed that FG2 was stable in the HPA active site. In vitro and in‐silico results showed that the studied phytoconstituents interacted with α‐amylase and their binding interaction resulted in reduction of the enzyme's activity. [ABSTRACT FROM AUTHOR]

To identify potent urease inhibitors, in the current study, a series of thioxothiazolidinyl-acetamides were designed and synthesized. The prepared compounds were characterized by spectroscopic techniques, including FTIR, 1HNMR, 13CNMR, and elemental analysis. In the enzymatic assessments, it was demonstrated that all derivatives had significant urease inhibition with IC50 values in the range of 1.473–9.274 µM in comparison with the positive control hydroxyurea (IC50 = 100.21 ± 2.5 µM) and thiourea (IC50 = 23.62 ± 0.84 µM). Compound 6i (N-benzyl-3-butyl-4-oxo-2-thioxothiazolidine-5-carboxamide) was the most active agent with an IC50 value of 1.473 µM. Additionally, kinetic investigation and in silico assessments of 6i was carried out to understand the type of inhibition and behavior of the most potent derivative within the binding site of the enzyme. Noteworthy, the anti-urease assay against P. vulgaris revealed 6e and 6i as the most active agents with IC50 values of 15.27 ± 2.40 and 17.78 ± 3.75 µg/mL, respectively. Antimicrobial evaluations of all compounds reveal that compounds 6n and 6o were the most potent antimicrobial agents against the standard and resistant S. aureus. 6n and 6o also showed 37 and 27% inhibition in the development of biofilm by S. aureus at 512 µg/ml. Furthermore, the MTT test showed no toxicity up to 100 µM. Taken together, the study suggests that the synthesized thioxothiazolidinyl-acetamides bases derivatives may serve as potential hits as urease inhibitors. [ABSTRACT FROM AUTHOR]

Context: Egypt has a high prevalence of the hepatitis C virus (HCV) genotype 4a (GT-4a). Unfortunately, the high resistance it exhibited still was not given the deserved attention in the scientific community. There is currently no consensus on the NS5A binding site because the crystal structure of HCV NS5A has not been resolved. The prediction of the binding modes of direct-acting antivirals (DAA) with the NS5A is a point of controversy due to the fact that several research groups presented different interaction models to elucidate the NS5A binding site. Consequently, a 3D model of HCV NS5A GT-4a was constructed and evaluated using molecular dynamics (MD) simulations. The generated model implies an intriguing new orientation of the AH relative to domain I. Additionally, the probable binding modes of marketed NS5A inhibitors were explored. MD simulations validated the stability of the predicted protein–ligand complexes. The suggested model predicts that daclatasvir and similar drugs bind symmetrically to HCV NS5A GT-4a. This will allow for the development of new NS5A-directed drugs, which may result in reduced resistance and/or a wider range of effectiveness against HCV. Methods: The 3D model of HCV NS5A GT-4a was constructed using the comparative modeling approach of the web-based application Robetta. Its stability was tested with 200-ns MD simulations using the Desmond package of Schrodinger. The OPLS2005 force field was assigned for minimization, and the RMSD, RMSF, and rGyr were tracked throughout the MD simulations. Fpocket was used to identify druggable protein pockets (cavities) over the simulation trajectories. The binding modes of marketed NS5A inhibitors were then generated and refined with the aid of docking predictions made by FRED and AutoDock Vina. The stability of these drugs in complex with GT-4a was investigated by using energetic and structural analyses over MD simulations. The Prime MM-GBSA (molecular mechanics/generalized Born surface area) method was used as a validation tool after the docking stage and for the averaged clusters after the MD simulation stage. We utilized PyMOL and VMD to visualize the data. [ABSTRACT FROM AUTHOR]

The primary focus of bisphosphonate medications is on targeting human farnesyl pyrophosphate synthase (hFPPS), an essential regulator of mammalian isoprenoids. Yet, these drugs encounter limitations due to their restricted "druglike" properties and their effectiveness primarily in treating skeletal disorders. In this study, we synthesized novel non-bisphosphonate compounds, using 4,4'-(ethane-1,2-diylbis(oxy))bis(3-methoxybenzaldehyde) (1) as a starting compound, with the aim of targeting hFPPS through a mixed binding approach. Among the various compounds tested, compounds 4a and 4b exhibited significant inhibition of hFPPS activity, with IC 50 values of 1.108 and 1.24 μM, respectively. Docking studies further revealed that both compounds bound within the allylic binding site and near the isopentenyl diphosphate (IPP) site within the hFPPS pocket. Molecular dynamic simulations were performed on the best docking pose of the most potent compound 4a to confirm the formation of a stable complex with hFPPS. In an in vivo study conducted on ovariectomized rats, various biochemical markers including osteocalcin, estradiol, osteoprotegerin, bone mineral content, and density were negatively impacted, while levels of bone specific alkaline phosphatase, receptor activator of nuclear factor kappa-Β ligand, serum/urinary calcium, and phosphate increased. Notably, compound 4a exhibited antiresorptive properties similar to zoledronate, effectively restoring most of the perturbed biochemical estimations. These findings suggest the potential of compound 4a , a non-bisphosphonate compound, as alternative therapeutic agents for combating osteoporosis. [Display omitted] • Synthesis of novel non-bisphosphonate compounds targeting hFPPS through a mixed binding approach. • Compounds 4a and 4b exhibited significant inhibition of hFPPS activity, with IC 50 values of 1.108 and 1.24 μM, respectively. • Docking studies further revealed that both compounds bound within the allylic binding site and near the isopentenyl diphosphate (IPP) site within the hFPPS pocket. • Molecular dynamic simulations were performed on the best docking pose of the most potent compound 4a to confirm the formation of a stable complex with hFPPS. • In vivo studies, compound 4a exhibited antiresorptive properties similar to zoledronate, the findings suggest that compound 4a is a non-bisphosphonate compound, as alternative therapeutic agents for combating osteoporosis. [ABSTRACT FROM AUTHOR]

Enzymes are one of the most important biological molecules in organisms. Systematic study of the functions of enzymes is of great value to scientific research and industrial application. In recent years, the methods of enzyme function prediction based on computer technology have been developing and improving. Based on this context, this paper summarizes the main computational-based methods of enzyme function prediction, including the binding sites, molecular docking, dynamic simulation, and molecular design. Meanwhile, the developing trend is discussed and prospected in this paper. [ABSTRACT FROM AUTHOR]

Many GTPases have been shown to utilize ATP too as the phosphoryl donor. Both GTP and ATP are important molecules in the cellular environments and play multiple and discrete functional role within the cells. In our present study, we showed that one of the purine metabolic enzymes Adenylosuccinate synthetase from Leishmania donovani (LdAdSS) which belongs to the BioD-superfamily of GTPases can also carry out the catalysis by hydrolysing ATP instead of its cognate substrate GTP albeit with less efficiency. Biochemical and biophysical studies indicated its ability to bind to ATP too but at a higher concentration of ATP compared to that of GTP. Sequence analysis and molecular dynamic simulations suggested that residues of the switch loop and the G4-G5 (593SAXD596) connected motif of LdAdSS plays a role in determining the nucleotide specificity. Though the crucial interaction between Asp596 and the nucleotide is broken when ATP is bound, interactions between the Ala594 and the adenine ring of ATP could still hold ATP in the GTP binding site. The results of the present study suggested that though LdAdSS is GTP specific, it still shows ATP hydrolysing activity. • Leishmania donovani Adenylosuccinate synthetase (LdAdSS), a GTPase can also utilize ATP for phosphoryl transfer onto IMP instead of GTP. • The binding affinity of LdAdSS with GTP is stronger than with ATP. • LdAdSS switch loop assumes a closed catalytically active conformation on GDP binding compared to the partially open conformation on ADP binding. • Residues belonging to the connected G4-G5 motif in LdAdSS may be a determinant of its purine base selectivity. [ABSTRACT FROM AUTHOR]

In this work, new derivatives of biphenyl pyrazole-benzofuran hybrids were designed, synthesized and evaluated in vitro through enzymatic assay for inhibitory effect against α-glucosidase activity. Newly identified inhibitors were found to be four to eighteen folds more active with IC50 values in the range of 40.6 ± 0.2–164.3 ± 1.8 µM, as compared to the standard drug acarbose (IC50 = 750.0 ± 10.0 μM). Limited Structure-activity relationship was established. A kinetic binding study indicated that most active compound 8e acted as the competitive inhibitors of α-glucosidase with Ki = 38 μM. Molecular docking has also been performed to find the interaction modes responsible for the desired inhibitory activity. As expected, all pharmacophoric features, used in the design of the hybrid, are involved in the interaction with the active site of the enzyme. In addition, molecular dynamic simulations showed compound 8e oriented vertically into the active site from mouth to the bottom and stabilized the enzyme domains by interacting with the interface of domain A and domain B and the back side of the active site while acarbose formed non-binding interaction with the residue belong to the domain A of the enzyme. [ABSTRACT FROM AUTHOR]

• Workflows of molecular docking and molecular dynamic simulation are overviewed. • Molecular docking reveals binding modes between myosin or myoglobin and additives. • Molecular dynamic simulation explores binding process of protein-additive complex. • Recent research of molecular methods in monitoring muscle quality is summarized. • Hydrogen and hydrophobic forces in protein-additive are proved by molecular methods. During storage and processing, muscle proteins, e.g. myosin and myoglobin, will inevitably undergo degeneration, which is thus accompanied by quality deterioration of muscle foods. Some exogenous additives have been widely used to interact with muscle proteins to stabilize the quality of muscle foods. Molecular docking and molecular dynamics simulation (MDS) are regarded as promising tools for recognizing dynamic molecular information at atomic level. Molecular docking and MDS can explore chemical bonds, specific binding sites, spatial structure changes, and binding energy between additives and muscle proteins. Development and workflow of molecular docking and MDS are systematically summarized in this review. Roles of molecular simulations are, for the first time, comprehensively discussed in recognizing the interaction details between muscle proteins and exogenous additives aimed for stabilizing color, texture, flavor, and other properties of muscle foods. Finally, research directions of molecular docking and MDS for improving the qualities of muscle foods are discussed. [ABSTRACT FROM AUTHOR]

• A set of 1,2,3-triazolyl-based metronidazole hybrids (7a-m) was synthesized from the reaction of 2-methyl-5-nitro-1-(prop‑2-yn-1-yl)−1H-imidazole with β-azido alcohols in the presence of [CuL] as catalyst. • The in vitro cytotoxic activity of the synthesized compounds 7a-m were investigated against human melanoma cell line A375, using MTT assay. • Among all the synthesized compounds, compound 7l was found to be the most potent derivative with IC 50 value of 62.5 µM. • The molecular docking studies and molecular dynamic simulation were carried out to obtain the binding mode of these derivatives in the binding site of receptor. • This work is helpful for researchers who planning to design and develop anticancer agents. In the current study, a set of 1,2,3-triazolyl-based metronidazole hybrids (7a-m) was synthesized from the reaction of 2-methyl-5-nitro-1-(prop‑2-yn-1-yl)-1H-imidazole with β-azido alcohols in the presence of [CuL] as catalyst. The chemical structures of the synthesized compounds were characterized using different spectroscopic techniques (IR, 1H NMR, 13C NMR, Mass) and elemental analysis. Then, the in vitro cytotoxic activity of the synthesized compounds 7a-m were investigated against human melanoma cell line A375, using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The cytotoxic results showed that these compounds have moderate anticancer activity compared to methotrexate as a reference drug. Among all the synthesized compounds, compound 7l was found to be the most potent derivative with IC 50 value of 62.5 µM. Finally, the molecular docking studies and molecular dynamic simulation were carried out to obtain the binding mode of these derivatives in the binding site of receptor. The results of docking studies were in good agreement with the in vitro cytotoxic results. [Display omitted] [ABSTRACT FROM AUTHOR]

Interleukin-1β (IL1β) is a keynote mediator of inflammation with diverse physiological functions, playing a fundamental role in memory and mood regulation. The pleiotropic effects of IL-1β have been proposed to be implicated in the pathogenesis and etiology of depression. Thus, targeting IL-1β offers an inimitable opportunity to develop new strategies for an alternative therapy to treat depression. The focus of this study is to find out the potential inhibitors against IL-1β. Since, there is no oral specific drug reported yet thus, demanding an urgent need to develop new immunomodulatory drugs to combat chronic diseases. In this study, ligand-based pharmacophore modeling integrated with virtual screening and molecular docking strategy was designed to identify novel compounds capable of inhibiting the interactions towards cognitive receptor IL-1RI. In this connection, a set of 30,000 compounds were screened by a developed pharmacophore model that led to the retrieval of 2043 molecules from the in-house library and ZINC Database. Primarily, specific binding regions for IL-1β inhibitors have been explored by blind docking studies. After the selection of the binding site, the hits identified as actives based on the 3D-pharmacophore model were assessed by molecular docking studies. In a stepwise screening, six potential virtual hits were shortlisted for molecular dynamic simulation to acquire insights into their dynamic behavior. The obtained results highlighted that these compounds are stabilized in the targeted pocket of IL-1β and possibly block the formation of an active heterocomplex, subsequently locking the associated signaling cascade. Further in vitro experiments confirmed the inhibitory potential of Compound-157 and compound-283 with the IC 50 of 1.6 ± 0.1 and 9.1 ± 1.7 µg/mL respectively. [Display omitted] • The study encompasses of Ligand-Based pharmacophore modelling, docking simulation and mechanistic analysis. • Interfacial key residues were identified to design IL-1β/IL-1RI potential inhibitors. • The mechanistic results highlighted that shortlisted six virtual hits are stabilized in the targeted pocket of IL-1β and possibly block the formation of active heterocomplex. • IL-1β inhibitors are found in good agreement withexperimental studies. [ABSTRACT FROM AUTHOR]